Terrorism in Southeast Asia

CRS Report for Congress
Terrorism in Southeast Asia
Updated February 14, 2006
Bruce Vaughn, Coordinator,
Emma Chanlett-Avery, Thomas Lum,
Mark Manyin, Larry Niksch
Foreign Affairs, Defense, and Trade Division

Congressional Research Service ˜ The Library of Congress

Terrorism in Southeast Asia
Since September 2001, the United States has been concerned with radical
Islamist groups in Southeast Asia, particularly those in the Philippines, Indonesia,
Malaysia, Thailand, and Singapore that are known to have ties to the Al Qaeda
terrorist network. Southeast Asia is a base for past, current, and possibly future Al
Qaeda operations. For nearly fifteen years, Al Qaeda has penetrated the region by
establishing local cells, training Southeast Asians in its camps in Afghanistan, and
by financing and cooperating with indigenous radical Islamist groups. Indonesia and
the southern Philippines have been particularly vulnerable to penetration by
anti-American Islamic terrorist groups.
Members of one indigenous network, Jemaah Islamiyah (JI), with extensive ties
to Al Qaeda, are known to have helped two of the September 11, 2001 hijackers and
have confessed to plotting and carrying out attacks against Western targets. These
include the deadliest terrorist attack since September 2001: the October 12, 2002
bombing in Bali, Indonesia, that killed approximately 200 people, mostly Westerners.
On September 9, 2004, a suicide bombing attack thought to be the work of JI struck
the Australian Embassy in Jakarta, killing 10 and wounding around 200. In October

2005, three suicide bombers exploded bombs within minutes of one another in Bali,

killing more than 20 people. These attacks suggest that JI remains capable of carrying
out relatively large-scale plots against Western targets, despite the arrest or death of
hundreds of JI members, including most of its known leadership.
To combat the threat, the Bush Administration has pressed countries in the
region to arrest suspected terrorist individuals and organizations, deployed over 1,000
troops to the southern Philippines to advise the Philippine military in their fight
against the violent Abu Sayyaf Group, launched a Regional Maritime Security
Initiative to enhance security in the Straits of Malacca, increased intelligence sharing
operations, restarted military-military relations with Indonesia (including restoring
International Military Education and Training [IMET]), and provided or requested
from Congress over $1 billion in aid to Indonesia and the Philippines.
The responses of countries in the region to both the threat and to the U.S.
reaction generally have varied with the intensity of their concerns about the threat to
their own stability and domestic politics. In general, Singapore, Malaysia, and the
Philippines were quick to crack down on militant groups and share intelligence with
the United States and Australia, whereas Indonesia began to do so only after attacks
or arrests revealed the severity of the threat to their citizens. That said, many
governments view increased American pressure and military presence in their region
with ambivalence because of the political sensitivity of the issue with both
mainstream Islamic and secular nationalist groups. Indonesia and Malaysia are
majority Muslim states while the Philippines and Thailand have sizeable, and
historically alienated and separatist-minded, Muslim minorities.
This report will be updated periodically.

Recent Developments..............................................1
Overview ........................................................2
The 9/11 Commission’s Recommendations.....................3
Background — The Rise of Islamic Militancy and Terrorism in Southeast Asia.3
The Rise of Al Qaeda in Southeast Asia............................4
The Jemaah Islamiyah Network.......................................5
History of Jemaah Islamiyah.....................................6
Jemaah Islamiyah’s Relationship to Al Qaeda........................7
Jemaah Islamiyah’s Size and Structure .............................8
Major Plots and Attacks .......................................10
The Trial of Baasyir.......................................12
Recent Activities.........................................13
Focus Countries..................................................14
Indonesia ...................................................14
Background .............................................14
Shifts in Jakarta’s Counter-Terrorism Policy....................15
Recent Developments.....................................17
The Philippines..............................................19
Phase One of U.S.-Philippine Military Cooperation..............20
The MILF and the MNLF..................................21
The Philippine Communist Party (CPP).......................21
Phase Two of U.S.-Philippine Military Cooperation?.............22
Thailand ....................................................23
Violence Continues in Southern Provinces.....................24
Central Government Response..............................24
Possible Foreign Involvement...............................25
Criticism of Thaksin’s Approach.............................26
Tension in Regional Relations...............................26
Thailand as a Convenient Base..............................27
A New Front in the War on Terror?...........................27
Malaysia ....................................................28
Recent Developments.....................................29
Singapore ...................................................30
Reformed Homeland Security Apparatus and Counterterror Strategy.31
Increased Intelligence Sharing...............................31
Bilateral and Multilateral Cooperation........................31
Australia ....................................................32
Cambodia and Burma: New Countries of Convenience?..............34
Options and Implications for U.S. Policy..............................35
Strategies for Combating Terrorism in Southeast Asia................35
Decapi t at i o n .............................................36
Military Options..........................................36

Public Diplomacy.........................................39
Multilateral Efforts........................................40
Indonesia ...................................................41
The Philippines..............................................43
Thailand ....................................................44
Role of Congress/Legislation........................................44
Indonesia ...................................................44
The “Leahy” Amendment Restriction on Military Aid............45
The Impact of 9/11........................................45
FY2005 Request for Indonesia, the Philippines, and Thailand..........46
Other CRS Products Dealing with Terrorism in Asia.....................48
Appendix A: U.S. Assistance to Indonesia, the Philippines, and Thailand
Since September 2001 .........................................49
Appendix B: Restrictions on Aid to Indonesia Since the “Leahy Amendment”
to the FY1992 Foreign Operations Appropriations Act................52
FY2002 Foreign Operations Appropriations — Seven Criteria for
IMET and FMF......................................53
FY2002 Supplemental Appropriation for Combating Terrorism
(P.L. 107-206/H.R. 4775)..............................53
FY2003 Foreign Operations Appropriations (P.L. 108-7/H.J.Res. 2)53
FY2004 Foreign Operations Appropriations (P.L. 108-199)........54
FY2005 Foreign Operations Appropriations (P.L. 108-447)........54
Appendix C: Maps...............................................56
List of Figures
Figure 1. Map of Jemaah Islamiyah’s Operations.........................9
Figure 2. Southeast Asia...........................................56
Figure 3. Indonesia...............................................57
Figure 4. Malaysia and Singapore....................................58
Figure 5. The Philippines..........................................59
Figure 6. Thailand................................................60
List of Tables
Table 1. U.S. Assistance to Indonesia, FY2002-FY2005..................49
Table 2. U.S. Assistance to the Philippines, FY2002-FY2005..............50
Table 3. U.S. Assistance to Thailand, FY2002-FY2005 ..................51

Terrorism in Southeast Asia
Developments in Late 2005/Early 2006
Over the past year, one of the most significant developments in the war against
radical Islamist militants in Southeast Asia has been the developing conflict in the
south of Thailand. Ongoing separatist violence in the southern provinces has
reinforced concern about indigenous and transnational terrorism in Thailand. These
developments have prompted action from Thai government officials and renewed
questions about links to broader networks. As the death toll has mounted, Prime
Minister Thaksin Shinawatra has come under fire for his handling of the situation.
Most regional observers stress that there is no convincing evidence to date of serious
Jemaah Islamiyah (JI) involvement in the attacks in the southern provinces. In
addition, the attacks have not targeted foreigners and have remained limited to a
particular geographical area.
Indonesia and the United States also made significant progress in reestablishing
closer bilateral ties that should help the two nations coordinate their efforts against
militants. This progress in the bilateral relationship was made possible by significant
policy developments by both the United States and Indonesia. President Yudhoyono,
elected in 2004, made the arrest of bomb makers Azahari Bin Husin and Noordin
Mahommad Top a key priority early in his administration. The death of Azahari Bin
Husin, as police closed in on him in East Java, as well as the arrest of more junior
militants thought to be close to Azahari’s associate Noordin Mahommad Top by
Special Anti-terror Detachment 88 of the Indonesian National Police has
demonstrated to many observers Indonesia’s continuing progress in its struggle with
extremists. Top remains at large.1
The Bush Administration also revealed details concerning an Al Qaeda plan,
which may have included recruits from Southeast Asia, to crash a highjacked airliner
into the U.S. Bank Tower in Los Angeles, California, though it is unclear how far this2
plan progressed to the operational stage. President Bush stated that the plot had been
“derailed in early 2002, when a Southeast Asian nation arrested a key Al Qaeda3

1 “Noordin’s Followers Still Hunted,” Media Indonesia, January 20, 2006.
2 “White house Reveals Plot to Use JI Recruits for Suicide Mission,” ABC (Australia) Radio,
February 10, 2006.
3 “Bush Gives New Details of 2002 Qaeda Plot to Attack Los Angeles,” The New York
Times, February 9, 2006.

Since the September 11, 2001 terrorist attacks, the United States has considered
Southeast Asia to be a “second front” in its global campaign against Islamist
terrorism.4 U.S. attention in the region has been focused on radical Islamist groups
in Southeast Asia, particularly the Jemaah Islamiyah terrorist network, that are
known or alleged to have ties to the Al Qaeda network. As detailed in the narrative
section of the Final Report of the National Commission on Terrorist Attacks Upon
the United States (known as the “9/11 Commission”), among other sources, many of
these groups threaten the status quo of the region by seeking to create independent
Islamic states in majority-Muslim areas, overthrow existing secular governments,
and/or establish a new supra-national Islamic state encompassing Indonesia,
Malaysia, Singapore, the southern Philippines, and southern Thailand.5 In pursuit of
these objectives, they have planned and carried out violent attacks against civilian
and non-civilian targets, including American and other Western institutions.
Additionally, Al Qaeda has used its Southeast Asia cells to help organize and finance
its global activities — including the September 11 attacks — and to provide safe
harbor to Al Qaeda operatives, such as the convicted organizer of the 1993 bombing
of the World Trade Center, Ramzi Yousef.
Combating anti-American terrorism in Southeast Asia presents the Bush
Administration and Congress with a delicate foreign policy problem. Most regional
governments also feel threatened by home-grown or imported Islamic militant groups
and therefore have ample incentive to cooperate with the U.S. antiterrorist campaign.
Despite mutual interests in combating terrorism, Southeast Asian governments have
to balance these security concerns with domestic political considerations. Although
proponents of violent, radical Islam remain a very small minority in Southeast Asia,
many governments view increased American pressure and military presence in their
region with ambivalence because of the political sensitivity of the issue with both
mainstream Islamic and secular nationalist groups. The rise in anti-American
sentiment propelled by both the U.S.-led invasion and occupation of Iraq and many
Southeast Asian Muslim’s perceptions of America’s stance on the Israeli-Palestinian
conflict as “blatantly pro-Israel”6 makes it even more difficult for most governments
to countenance an overt U.S. role in their internal security. The challenge is to find
a way to confront the terrorist elements without turning them into heroes or martyrs
in the broader Southeast Asian Islamic community. Furthermore, the continued
activities of Al Qaeda and Jemaah Islamiyah will require a coordinated, international
response in a region where multinational institutions and cooperation are weak.

4 In the days after the September 11 attacks, at least one senior Pentagon official floated the
idea of taking military action against terrorist targets in Southeast Asia as a “surprise”
alternative to attacking Afghanistan. The 9/11 Commission Report. Final Report of the
National Commission on Terrorist Attacks Upon the United States (New York: W.W.
Norton & Co., 2004), p. 559, note 75; Douglas Feith, “A War Plan That Cast A Wide Net,”
Washington Post, August 7, 2004.
5 The 9/11 Commission Report.
6 Daljit Singh,”The Terrorist Threat in Southeast Asia,” Regional Outlook; 2003-2004.

On December 17, 2004, Congressional legislation, that seeks to address the war
against terrorism in ways that would affect its prosecution in Southeast Asia, became
Public Law 108-458, the Intelligence Reform and Terrorism Prevention Act of 2004.
P.L. 108-458 addresses a number of issues identified by the 9/11 Commission Report
including the need to identify and eliminate terrorist sanctuaries, to increase
engagement between America and Muslim peoples, to support public education in
Muslim states, to foster scholastic exchange with Muslim states, to promote
economic policies to encourage development of open societies, to engage foreign
governments in developing a comprehensive multilateral strategy to fight terrorism,
and to track terrorist financing among other provisions.
Background — The Rise of Islamic Militancy and
Terrorism in Southeast Asia
Southeast Asia has been the home of indigenous Islamic militant groups for
decades. Traditionally, the linkages among these groups were relatively weak, and
most operated only in their own country or islands, focusing on domestic issues such
as promoting the adoption of Islamic law (sharia) and seeking independence from
central government control. The Philippines has had a violent Muslim separatist
movement for more than a century. The Moros of Mindanao and the Sulu
Archipelago, including the island of Jolo, fought a stubborn, bloody, and ultimately
futile insurgency against the American occupation of the southern Philippines
following the Spanish American War (1898). Until recently, however, the activities
of several Muslim extremist groups in the Philippines had been confined mainly to
the relatively isolated Muslim-majority regions in the South.
In Indonesia, various schools of Islamic thought have competed for followers
and public attention, but most have not called for an Islamic state. The more radical
groups, which had their roots in anti-Dutch guerilla activities, effectively were kept
in check by strong leadership from Presidents Sukarno (1950-1965) and especially
Suharto (1967-1998). Moderate Islamic groups formed the main legal opposition to
the Suharto regime which ended in May 1998. Since Suharto’s fall, religious
consciousness has been on the rise among Indonesian Muslims, giving greater
political space for radical groups and their violent fringe to operate, at times openly.
In Malaysia, the late 1990s saw a potentially significant electoral swing toward
a radical Islamist party, Parti Islam se-Malaysia (PAS). However, PAS suffered
major setbacks in parliamentary elections in early 2004. The results appear to
indicate that mainstream Islam in Malaysia has reasserted its moderate character.
Prime Minister Abdullah Badawi, who is himself a respected Islamic Scholar, has
demonstrated Malaysia’s moderate Islamic approach since replacing former Prime
Minister Mahathir Mohammad.
The emergence of radical Islamic movements in Southeast Asia in the 1990s can
be traced to the conjunction of several phenomena. Among these were reaction to
globalization — which has been particularly associated with the United States in the
minds of regional elites — frustration with repression by secularist governments, the
desire to create a pan-Islamic Southeast Asia, reaction to the Israeli occupation in the

West Bank and Gaza Strip, and the arrival of terrorist veterans of years of fighting
in Afghanistan. The forging of connections between Al Qaeda and domestic radical
Islamic groups in Southeast Asia is part of this trend.
The Rise of Al Qaeda in Southeast Asia7
Beginning in the early-to-mid 1990s the Al Qaeda terrorist network made
significant inroads into the Southeast Asia region. Al Qaeda’s Southeast Asian
operatives — who have been primarily of Middle Eastern origin — appear to have
performed three primary tasks. First, they set up local cells, predominantly headed
by Arab members of Al Qaeda, that served as regional offices supporting the
network’s global operations. These cells have exploited the region’s generally lax
border controls to hold meetings in Southeast Asia to plan attacks against Western
targets, host operatives transiting through Southeast Asia, and provide safe haven for
other operatives fleeing U.S. intelligence services. Al Qaeda’s Manila cell, which
was founded in the early 1990s by a brother-in-law of Osama bin Laden, was
particularly active in the early-mid-1990s. Under the leadership of Ramzi Yousef,
who fled to Manila after coordinating the 1993 bombing of the World Trade Center
in New York, the cell plotted to blow up 11 airliners in a two-day period (what was
known as the “Bojinka” plan), crash a hijacked airliner into the Central Intelligence
Agency’s headquarters, and assassinate the Pope during his visit to the Philippines
in early 1995. Yousef was assisted in Manila for a time by his uncle, Khalid Sheikh
Mohammed, the alleged mastermind of the September 11, 2001 attacks.8 In the late
1990s, the locus of Al Qaeda’s Southeast Asia activity appears to have moved to
Malaysia, Singapore, and — most recently — Indonesia. In 1999 and 2000, Kuala
Lumpur and Bangkok were the sites for important strategy meetings among some of
the September 11 plotters.9 Al Qaeda’s leadership also has taken advantage of
Southeast Asia’s generally lax financial controls to use various countries in the
region as places to raise, transmit, and launder the network’s funds. By 2002,
according to one prominent expert on Al Qaeda, roughly one-fifth of Al Qaeda’s
organizational strength was centered in Southeast Asia.10
Second, over time, Al Qaeda Southeast Asian operatives helped create what may
be Southeast Asia’s first indigenous regional terrorist network, Jemaah Islamiyah

7 For more on Al Qaeda, see CRS Report RL32223, Foreign Terrorist Organizations, by
Audrey Kurth Cronin, et al.; CRS Report RS21529, Al Qaeda after the Iraq Conflict, by
Audrey Kurth Cronin; and CRS Report RL31119, Terrorism: Near Eastern Groups and
State Sponsors, 2002, by Kenneth Katzman.
8 Filipino police discovered the Bojinka plot, which was in the final stages, in January 1995
only because a fire broke out in Yousef’s apartment, filling it with poisonous gas from the
bomb-making chemicals. Yousef fled to Malaysia, was arrested in Pakistan, and extradited
to the United States, where he was sentenced to life imprisonment for his role in the 1993
bombing and the Bojinka plot. See The 9/11 Commission Report, p.147-48.
9 For examples of how the September 11 plot organizers traveled relatively freely throughout
Southeast Asia to hold meetings and case flights, see The 9/11 Commission Report, p. 156-


10 Report to the UN Security Council by the Security Council Monitoring Group, ‘1267'
Committee, Security Council Report S/2003/669, July 7, 2003, p. 15.

(JI), that has plotted attacks against Western targets. Jemaah Islamiyah is suspected
of carrying out the October 12, 2002 bombing in Bali, Indonesia, that killed
approximately 200 people, mostly Western tourists. Although JI does not appear to
be subordinate to Al Qaeda, the two networks have cooperated extensively.
Third, Al Qaeda’s local cells worked to cooperate with indigenous radical
Islamic groups by providing them with money and training. Until it was broken up
in the mid-1990s, Al Qaeda’s Manila cell provided extensive financial assistance to
Moro militants such as the Abu Sayyaf Group and the Moro Islamic Liberation Front
(MILF). Thousands of militants have reportedly been trained in Al Qaeda camps in
Afghanistan or in the camps of Filipino, Indonesian, and Malaysian groups that
opened their doors to Al Qaeda. Al Qaeda reportedly provided funds and trainers for
camps operated by local groups in Indonesia, Malaysia, and the Philippines.
Indonesian intelligence officials also accuse Al Qaeda of sending fighters to
participate in and foment the Muslim attacks on Christians in the Malukus and on
Sulawesi that began in 2000.11 Al Qaeda operatives’ task was made easier by several
factors: the withdrawal of foreign state sponsors, most notably Libya, that had
supported some local groups in the 1970s and 1980s; the personal relationships that
had been established during the 1980s, when many Southeast Asian radicals had
fought as mujahideen in Afghanistan; and the weak central government control,
endemic corruption, porous borders, minimal visa requirements, extensive network
of Islamic charities, and lax financial controls of some countries, most notably
Indonesia and the Philippines.12
Over time, Al Qaeda’s presence in the region has had the effect of
professionalizing local groups and forging ties among them — and between them and
Al Qaeda — so that they can better cooperate. In many cases, this cooperation has
taken the form of ad hoc arrangements of convenience, such as helping procure
weapons and explosives.
The Jemaah Islamiyah Network
In the weeks after the September 11 terrorist attacks, a pan-Asian terrorist
network with extensive links to Al Qaeda was uncovered. The network, known as
Jemaah Islamiyah (Islamic Group), has cells in Malaysia, Singapore, Indonesia, the
Philippines, Australia, Thailand, and Pakistan. Its goals range from establishing an
Islamic regime in Indonesia, to establishing an Islamic Khaliphate over Muslim
regions of Southeast Asia and northern Australia, to waging jihad against the West.
There appears to be considerable debate within the organization about which of these
goals to pursue and prioritize, with different JI factions preferring different
objectives. Jemaah Islamiyah (JI) leaders have formed alliances with other militant
Islamist groups to share resources for training, arms procurement, financial
assistance, and to promote cooperation in carrying out attacks. Specifically, there is

11 Zachary Abuza, “Terrorism in Southeast Asia,” in National Bureau of Asian Research,
Strategic Asia 2002-3.
12 Zachary Abuza, “Tentacles of Terror,” unpublished October 21, 2002 draft, p. 3.

considerable evidence that JI has engaged in joint operations and training with the
Filipino separatist group, the Moro Islamic Liberation Front (MILF).13 Some reports
indicate that JI camps may continue to operate in MILF territory in Mindanao.14
Indeed, there is some evidence that such cooperation has increased since 2002, when
arrests and other counter-terror actions began to take its toll on JI, forcing it to adapt
and form closer working relationships with local groups.Within Indonesia, the
network has created and/or trained local radical groups that have been involved in
sectarian conflict in the country’s outer islands.
In October 2002, shortly after the attack in Bali, the United States designated JI
as a foreign terrorist organization.15 Thereafter, the United Nations Security Council
added the network to its own list of terrorist groups, a move requiring all U.N.
members to freeze the organization’s assets, deny it access to funding, and prevent
its members from entering or traveling through their territories. Since December
2001, over 250 suspected and admitted JI members, including a number of key
leaders have been arrested. Many of these arrests have been due to more extensive
intelligence sharing among national police forces. The Bali bombing spurred
Indonesian officials to reverse their previous reluctance to take on the Jemaah
Islamiyah network, thought the Indonesian government has not banned the
History of Jemaah Islamiyah
The origins of the Jemaah Islamiyah network stretch back to the 1960s, when
its co-founders, clerics Abu Bakar Baasyir and Abdullah Sungkar, began demanding
the establishment of sharia law in Indonesia. The two considered themselves the
ideological heirs of the founder of the Darul Islam movement, the Muslim guerilla
force that during the 1940s fought both imperial Dutch troops and the secularist
Indonesian forces of Sukarno, Indonesia’s founding President who ruled from
1950-65. In the 1970s, the two men established Al Mukmin, a boarding school in
Solo, on the main island of Java, that preached the puritanical Wahhabi interpretation
of Islam founded and propagated in Saudi Arabia. Many suspected JI activists who
have been arrested are Al Mukmin alums. In 1985, Baasyir and Sungkar fled to
Malaysia, where they set up a base of operations and helped send Indonesians and
Malaysians to Afghanistan, first to fight the Soviets and later to train in Al Qaeda
camps. Sungkar and Baasyir formed JI in 1993 or 1994, and steadily began setting
up a sophisticated organizational structure and actively planning and recruiting for
terrorism in Southeast Asia. Sometime in the mid-1990s, Sungkar and Baasyir
apparently began to actively coordinate with Al Qaeda.

13 See, for instance, Singapore Home Affairs Ministry White Paper, The Jemaah Islamiyah
Arrests and the Threat of Terrorism, January 7, 2003, p.7-9,
[http://www.mha.gov.sg/wp/complete.zip]; Abuza, “Terrorism in Southeast Asia,” in
National Bureau of Asian Research, Strategic Asia 2002-3.
14 Ellen Nakashima, “Indonesian Militants ‘Keep Regenerating’,” Washington Post, March

25, 2004.

15 For more on the designation process, see CRS Report RL32120, The “FTO List” and
Congress: Sanctioning Designated Foreign Terrorist Organizations, by Audrey Kurth

The fall of Indonesia’s Suharto regime in 1998 provided a major boost to JI.
Almost overnight, formerly restricted Muslim groups from across the spectrum were
able to operate. Baasyir and Sungkar returned to Solo, preaching and organizing in
relative openness there. Simultaneously, Jakarta’s ability to maintain order in
Indonesia’s outer islands decreased dramatically, and long-repressed tensions
between Muslims and Christians began to erupt. In 1999 and 2000, the outbreak of
sectarian violence in Ambon (in the Malukus) and Poso (on Sulawesi) provided JI
with critical opportunities to recruit, train, and fund local mujahadeen fighters to
participate in the sectarian conflict, in which hundreds died.16 After the violence
ebbed, many of these jihadis became active members in Baasyir’s network. In 2000,
the network carried out bombings in Jakarta, Manila, and Thailand.
Jemaah Islamiyah’s Relationship to Al Qaeda
There has been considerable debate over the relationship between Jemaah
Islamiyah and Al Qaeda. Although many analysts at first assumed that JI is Al
Qaeda’s Southeast Asian affiliate, reporting — including leaks from interrogations
of captured JI and Al Qaeda operatives — have shown that the two groups are
discrete organizations with differing, though often overlapping, agendas.17 Whereas
Al Qaeda’s focus is global and definitively targets Westerners and Western
institutions, Jemaah Islamiyah is focused on radicalizing Muslim Southeast Asia
(starting with Indonesia) and some JI leaders are said to feel that attacking Western
targets — as Osama bin Laden has urged — will undermine this goal.
That said, the two networks have developed a highly symbiotic relationship.
There is some overlap in membership. They have shared training camps in Pakistan,
Afghanistan, and Mindanao. Al Qaeda has provided JI with considerable financial
support.18 They shared personnel, such as when JI sent an operative with scientific
expertise to Afghanistan to try to develop an anthrax program for Al Qaeda.19 The
two networks have jointly planned operations — including the September 11 attacks
— and reportedly have conducted attacks in Southeast Asia jointly.20 Often, these
operations took the form of Al Qaeda’s providing funding and technical expertise,
while JI procured local materials (such as bomb-making materials) and located

16 Sidney Jones, “Indonesia Backgrounder: Jihad in Central Sulawesi,” International Crisis
Group Report No74, February 3, 2004.
17 Zachary Abuza, “Funding Terrorism in Southeast Asia: The Financial Network of Al
Qaeda and Jemaah Islamiyah,” NBR Analysis, December 2003, p.11-12; The 9/11
Commission Report, p. 150-52.
18 Sidney Jones, “Jemaah Islamiyah in South East Asia: Damaged but Still Dangerous,”
International Crisis Group Report No 63, August 26, 2003, p. 1; Abuza, “Funding Terrorism
in Southeast Asia,” p. 9.
19 The 9/11 Commission Report, p. 151. Yazid Sufaat is the individual JI sent to Kandahar.
20 Al Qaeda and JI leaders met in Southeast Asia for at least two critical meetings: One in
January 2000 in Kuala Lumpur, during which plans for the attack on the USS Cole and the
September 11 hijackings were discussed. The other occurred in Bangkok in January 2002,
during which an Al Qaeda representative reportedly sat in on the planning of the Bali

operatives.21 Riduan Isamuddin (also known as Hambali), appears to have been a
critical coordinator in these joint operations, and his arrest in 2003 may have
curtailed JI-Al Qaeda cooperation, which according to one prominent expert, Sidney
Jones, were closest between 1997 and 2002.22 Finally, terrorist attacks in 2003 and
2004 in Morocco, Turkey, and Spain may indicate that Al Qaeda’s anti-Western
ideology simply is inspiring individuals and local groups — such as JI and its
affiliates — to undertake terrorist acts.
Jemaah Islamiyah’s Size and Structure
The total number of core Jemaah Islamiyah members has been estimated to
range from 500 to several thousand.23 Its influence transcends these numbers,
however. Many more men have been educated at JI-run pesantrens (religious
boarding schools), where the Baasyir and Sungkar’s radical interpretation of Islam
is taught. JI also has avidly sought out alliances — which at times have been ad hoc
— with a loose network of like-minded organizations, and JI-run training camps
have upgraded the military skills and ideological fervor of smaller, localized groups.
In 1999, JI leaders reportedly established the Rabitatul Mujihidin (RM) of regional
jihadi groups, including representatives from Aceh, Thailand, Burma and
Bangladesh, with the goal of bringing new organizations into the JI family and to
coordinate jihad activities such as carrying out attacks, procuring arms, sharing
training resources, and pooling finances. The RM is thought to have held three
meetings, all in Malaysia between 1999 and late 2000.
Interrogations of Jemaah Islamiyah members have revealed a highly formalized
command structure, at least during the early part of the decade. At its peak
organizational strength in 2000 and 2001, JI was led by a five-member Regional
Advisory Council chaired by Hambali, an important coordinator of JI and Al Qaeda
activities. Baasyir and Sungkar served as spiritual advisors. Beneath the council
were several functional committees and four mantiqis (loosely translated as regional
brigades) that were defined not only by geography but also by functional roles,
including fundraising, religious indoctrination, military training, and weapons
procurement (see Figure 1). Each mantiqi, in turn, was subdivided into at least three24
additional layers: battalions, platoons, and squads.
However, in practice, JI appears to function in a much less centralized fashion
than this structure might imply. The network’s goal of developing indigenous jihadis
meant that JI members often have worked with and/or created local groups outside
its control. It often is difficult to sort out the overlap among JI and other radical
groups. Additionally, regional leaders appear to have had a fair amount of autonomy,
and by necessity many of the individual cells were compartmentalized from one

21 The 9/11 Commission Report, p.151.
22 Jones, “The Changing Nature of Jemaah Islamiya,” p.172-74.
23 Zachary Abuza, “The War on Terrorism in Southeast Asia,” in Strategic Asia 2003-04,
(Seattle, WA: National Bureau of Asian Research, 2003), p. 333; Jones, “Jemaah Islamiyah
in South East Asia,” p. ii.
24 Jones, “Jemaah Islamiyah in South East Asia,” p. 27-28.

another. This means that no single individual is indispensable. The arrest of many
if not most of JI’s top leaders appears to have accentuated these decentralized
tendencies by disrupting the network’s command and control structure.25 Finally, JI’s
structure has expanded and contracted in response to internal and external
developments. Indonesian expert Sidney Jones has written that since 2002, a more
flexible structure, “better suited for an organization under siege,” undoubtedly has
evolved.26 In January 2006, Noordin Muhammad Top declared himself the leader of
a new group Tandzim Qoedatul Jihad. This appeared to confirm earlier views that JI
had split into different factions.27

25 Jones, “Jihad in Central Sulawesi,” p.24; April 2004 e-mail correspondence with Zachary
26 Jones,”The Changing Nature of Jemaah Islamiya,” p.170.
27 Elizabeth Mills, “Notorius Malaysian Bomber Proclaims Himself Head of New South-
East Asian Terror Outfit,” Global Insight, January 30, 2006.

Figure 1. Map of Jemaah Islamiyah’s Operations

Al Qaeda
(Af ghanistan/ Pakistan)
Abu Dhabi
Al Qaeda
(Middle East)
Indonesians andMantiqi 3
Malaysians traveledthe Philippines, Brunei,
to Afghanistan andeastern Malaysia,
Pakistan to fight theKalimantan & Sulawesi
Soviet occupation(Indonesia)
and/or train in Al
Qaeda camps.Mantiqi 1
Malaysia, Singapore,
iki/CRS-RL31672Funding networks, withMantiqi 4southern Thailand
g/wlinks to financial centersPapua & Australia
s.orin Abu Dhabi and other
leakparts of the United ArabEmirates.Jemaah Islamiyah
Mantiqi 2
Jemaah Islamiyah's OperationsJava & Sumatra (Indonesia)
Source: Reproduced from Zachary Abuza, "The War on Terrorism in Southeast Asia," in Richard J.. Ellings and Aaron L. Friedberg with Michael Wills,
STRATEGIC ASIA 2003-04: FRAGILITY AND CRISIS, by permission from The National Bureau of Asian Research.

JI’s continued attacks in 2003 and 2004 indicates that it retains the ability to
carry out attacks despite the arrest or death of almost all of its former leaders.
Apparently, the network either has reconstituted its leadership, or is able to function
without central direction, or both. In the summer of 2004, Singapore’s Home Affairs
Minister Wong Kan-Seng indicated that JI is planning new attacks and has
replenished its leadership.28 The latter development appeared to be reinforced from
interrogations of suspected JI militants who reportedly told of training camps that
continued to be operating in Mindanao, which some analysts say are JI’s current
strategic base of operations and training.
The breakdown of JI’s hierarchy also may have exacerbated what one report, by
the International Crisis Group, has described as tensions between two factions over
the best strategy for waging jihad. A minority group, led by Hambali, is interested
in focusing on a broader anti-Western agenda similar to al Qaeda, and in effecting
change in the near term. For instance, in the ongoing sectarian strife on the island
of Sulawesi, many of these JI members have formed and aided a militia called
Mujahidin Kompak that has set up training camps and has sought to get recruits into
military battle as quickly as possible. Opposing this faction is a majority group
within JI, depicted as the “bureaucrats,” that sees these tactics as undermining its
preferred, longer-term strategy of building up military capacity and using religious
proselytization to create a mass base sufficient to support an Islamic revolution.29
The implication is that JI may not be as monolithic as commonly assumed, though
it is important to point out that the two camps’ goals are not necessarily mutually
exclusive. Hambali, for instance, is believed to have overseen JI’s involvement in the
communal conflicts in the Malukus in 1999. Likewise, there appears to be divisions
among JI members about geographic objectives, with some seeking to establish a
Islamic state in Southeast Asia and others focused solely on establishing an Islamic
state in Indonesia.30
Major Plots and Attacks
Jemaah Islamiyah first came to public attention in December 2001, when
Singapore’s Internal Security Department (ISD) raided two Singapore cells for
plotting bombing attacks against American, Australian, British, and Israeli
installations and citizens in Singapore. A video tape subsequently found by U.S.
forces in Afghanistan confirmed the Al Qaeda connection with the plot. Follow-on
arrests netted plotters in Malaysia and the Philippines. Reportedly, the JI cell in
Malaysia coordinated the plot, including the procurement of bomb-making materials,
preparing forged travel documents, and communications with Al Qaeda.

28 Amit Chanda, “Officials in Singapore Warn that JI has Replenished Leadership,” WMRC
Daily Analysis, August 5, 2004.
29 Jones, “Jihad in Central Sulawesi,” p. 24-25. The 9/11 Commission Report (note 26 on
p.490) notes that during his interrogation, Khalid Sheikh Mohammed, Baasyir criticized
Hambali for focusing too heavily on Al Qaeda’s broader, global agenda at the expense of
accomplishing JI’s aims in Indonesia and Malaysia.
30 Jones, “The Changing nature of Jemaah Islamiya,” p.171-72.

Subsequent investigation and arrests led the FBI to link Jemaah Islamiyah to the
September 11 attack on the United States. Two of the September 11 hijackers and
Zacarias Moussaoui, who pled guilty in April 2005 to U.S. charges of involvement
in the September 11 plot, apparently visited Malaysia and met with cell members in
2000. Additionally, the FBI claims that Malaysian cell members provided
Moussaoui with $35,000 and a business reference.
In June 2002, the Indonesian police arrested a suspected Al Qaeda leader,
Kuwaiti national Omar al-Farouq, at the request of the CIA and turned him over to
the U.S. military. After three months of interrogation, al-Farouq reportedly confessed
that he was Al Qaeda’s senior representative in Southeast Asia and disclosed plans
for other terrorist attacks against U.S. interests in the region. These included a joint
Al Qaeda/JI plan to conduct simultaneous car/truck bomb attacks against U.S.
interests in Indonesia, Malaysia, Singapore, the Philippines, Thailand, Taiwan,
Vietnam, and Cambodia around the one-year anniversary of the September 11
attacks.31 On the basis of this and other information, in September 2002, the Bush
Administration closed U.S. embassies in several countries for several days and raised
the overall U.S. threat level from “elevated” (yellow) to “high”(orange). Under
interrogation, Al-Farouq reportedly identified Baasyir as the spiritual leader of JI and
one of the organizers of the planned September 2002 attacks. For months, Malaysia
and Singapore had also accused Baasyir of being a leader of JI and had joined with
the United States in asking Indonesia to arrest him. In July 2005, Al-Farouq and
other suspected Al Qaeda members escaped from a U.S. military detention center in
Bagram, Afghanistan.32
The Bali Bombings. The danger posed by Jemaah Islamiyah and Al Qaeda
was underscored by the October 12, 2002 bombings in a nightclub district in Bali
frequented by western tourists. Synchronized bomb blasts and subsequent fires in a
nightclub district popular with young tourists and backpackers killed approximately
200 and injured some 300, mainly Australians and Indonesians, but also including
several Americans as well as Canadians, Europeans, and Japanese. The bombings,
the most deadly since the September 11, 2001 attacks in the United States, appeared
to mark a shift in JI’s strategy; the FBI has reported that in early 2002, senior JI
leaders — meeting in Thailand — decided to attack “softer targets” in Asia such as33
tourist sites frequented by Westerners. The focus on soft targets was returned to in
a second Bali bombing in October 2005. In that attack, at least 20 were killed and
over 100 injured, including 2 Americans and other Westerners, when three suicide
bombers attacked restaurants frequented by foreigners.34

31 Romesh Ratnesar, “Confessions of an Al-Qaeda Terrorist,” Time, September 23, 2002.
32 Eric Schmidt and Time Golden, “Details Emerge on a Brazen Escape in Afghanistan,”
New York Times, December 4, 2005.
33 Jay Solomon and James Hookway, “Bali Bomb Suspect Used Thailand as Staging Area,”
The Wall Street Journal, November 7, 2002.
34 R. Pura and L. Lopez, “Bali Blast Signals Militants Rebirth,” The Wall Street Journal,
October 3, 2005.

The Bali bombing spurred the Indonesian government to reverse its previous
reluctance to investigate JI. In the days after the blasts, senior Indonesian officials
acknowledged for the first time that Al Qaeda was operating in Indonesia and was
cooperating with JI.35 With the substantial aid of Australian and U.S. investigators,
Indonesian police have arrested several suspects, including Ali Gufron (also known
as Mukhlas), who is thought to be a senior JI commander and an associate of Baasyir.
Trials began in the spring and summer of 2003. On August 7, 2003, Islamic militant
Amrozi was sentenced to death by an Indonesian court for his involvement in the
Bali bombings. The government also announced a series of decrees that strengthen
the hand of the government in dealing with terrorism. In the days after the bombing,
Indonesia also formally supported the United States’ petition to the U.N. that Jemaah
Islamiyah be added to the U.N.’s list of terrorist groups.
The Trial of Baasyir. The Bali bombing also spurred the Indonesian
government to arrest Baasyir. He had long been viewed by U.S. officials as directly
involved with terrorism, but until the Bali bombing the Indonesian government had
refused to acknowledge his role or arrest him for fear of an anti-government
backlash. Although several of those charged with carrying out the Bali attack have
implicated Baasyir in the attack, the lack of sufficient evidence led Indonesian
authorities to charge him with involvement in past terrorist plots, including an
attempt to assassinate Megawati Sukaranoputri when she was Vice-President.
Baasyir’s highly publicized trial began in the spring of 2003. Baasyir denies leading
JI, though he acknowledges training at his Al Mukmin school all of the 13 suspects
arrested in Singapore in December 2001.36 On September 3, 2003, an Indonesian
court convicted him of plotting to overthrow the Indonesian government but dropped
more serious charges, including accusations that he is the leader of Jemaah Islamiyah.
Baasyir was sentenced to four years in jail. Prosecutors had asked for a 15-year
sentence. In March 2004, the Indonesian Supreme Court reduced Baasyir’s sentence.
He was to be released in May 2004, but at the end of April, Indonesian police
announced that Baasyir had been declared a suspect in other terrorist attacks, which
allowed them to continue his detention. Some prominent Indonesians have said the
move came as a result of pressure from the United States and Australia.37 Ahmad
Syafii Maarif, leader of Muhammadiyah, is reported to have said that then-U.S.
Ambassador to Indonesia Ralph Boyce had asked for help in persuading then-38
President Megawati to keep Baasyir in detention.
As the trial against Baasyir proceeded it appeared that the prosecution had a
weak case against Baasyir. The prosecution called for only a reduced sentence of
eight years in jail instead of the death penalty. This may have been the result of the

35 Ellen Nakashima and Alan Sipress, “Al Qaeda Linked to Blast by Official,” Washington
Post, October 15, 2002.
36 Abuza, “Tentacles of Terror,” p.72.
37 Raymond Bonner, “U.S. Pressure to Hold Militant Sets Off Outcry in Indonesia,” New
York Times, April 20, 2004.
38 “Baasyir Nonviolent: Muhammadiyah Chief,” The Jakarta Post, January 14, 2005.

prosecution’s inability to get key witnesses to testify against Baasyir.39 None of the
32 witnesses for the prosecution directly connected Baasyir with the Bali or Marriott
bombings, though some did connect Baasyir to JI training camps in the southern
Philippines.40 Only one witness testified that Baasyir was the leader of JI.41 Baasyir
was sentenced to 30 months’ imprisonment for conspiracy in the 2002 Bali bombings
in April 2004. His sentence was reduced in August 2005 by four months and 15 days.
He is now set to be released in June 2006.42
Recent Activities. JI’s major plots and attacks appear to operate in roughly
one-year cycles — the Christmas bombings of 2000, the plot against the targets in
Singapore in late 2001, the Bali bombing in October 2002, the Marriott bombing in
August 2003, the bombing of the Australian Embassy in September 2004 and the
Bali II bombing of October 2005. Following this pattern in October 2005, three
suicide bombers exploded bombs within minutes of one another in Bali, killing more
than 20 people (mostly Indonesian) and wounding more than 100. Two Malaysian
members of JI, Azahari Husin and Noordin Mohammad Top, were sought for their
role in planning the bombing of the Australian Embassy and the and the 2005 Bali
bombing. In November 2005, Indonesian police cornered Azahari in Batu, East Java.
He died in the ensuing shootout. Noordin remains at large. Citing the threat from JI,
the State Department as of mid-January 2006 advised U.S. citizens against non-
essential travel to Indonesia, and warned that Americans traveling in the Philippines
should “observe vigilant personal security precautions.”
Focus Countries
Recent Developments. Bilateral relations between the United States and
Indonesia improved dramatically in 2005. This was largely the product of a
successful democratic process in 2004 that led to the election of President Susilo
Bambang Yudhoyono and an increased appreciation of Indonesia’s democratic
evolution in the United States. This, and the importance of Indonesia to the war
against violent Islamic extremists in Southeast Asia and Indonesia’s regional
geopolitical importance led the Bush Administration to decide in February 2005 to
allow Indonesia to participate in International Military Education and Training
(IMET). This was followed by a May 2005 decision to restart non-lethal Foreign
Military Sales (FMS) to Indonesia and a November 2005 decision to waive Foreign
Military Financing (FMF) restrictions due to U.S. national security concerns.43

39 “Bashir: A Strong Chance to walk Free,” Australian Associated Press, February 9, 2005.
40 Sian Powell, “Call for Baasyir Jail Term,” The Australian, February 9, 2005.
41 “Indonesian Prosecutors Ask for Eight-Year Jail Sentence for Bashir,” Voice of America,
February 8, 2005.
42 “Indonesian Court Told JI Leader Not Tied to Bali Bombing,” COMTEX, January 4, 2006.
43 State Department, Office of the Spokesman, Washington, DC, “Taken Question at Daily

JI’s operations in Indonesia appeared to be significantly degraded by Indonesian
counter terror efforts in 2005 though it demonstrated its continuing lethality with a
second Bali blast in October 2005. Leading JI bomb maker Azahari Husin apparently
killed himself to avoid capture by the U.S. trained special counter terror unit
Detachment 88 as the unit closed in on him in November 2005.44 The Christmas 2000
bombings, the Bali bombings of 2002 and 2005, as well as the bombing of the
Marriott Hotel and the Australian Embassy in Jakarta are the most high profile
bombings attributed to JI in Indonesia.45 His associate, JI bomb maker Noordin
Muhammad Top, escaped capture at that time and is still at large. In January 2006,
Special Detachment 88 Anti-terror Police arrested four individuals believed to be
Top accomplices.46 Sydney Jones has described JI as having split into a bombing
faction of approximately 50, that is divided into cells of 5 to 10 people focused on
Java, and a JI “mainstream” of approximately 1,000 which does not share the
enthusiasm of the first group for bombings but is focused on establishing an Islamic
state in Indonesia.47
Top has been reported to now lead a new group, Tandzim Qoedatul Jihad. It is
not clear to what extent this group has ties to JI. It is thought that Top is continuing
to form Istimata Brigades or suicide bomb teams. It has also been reported that Top
has established a new organizational structure, the Ma’sul, at the district level and
that it is at this level that suicide bombers are being recruited.48 Top’s focus on
bombing “Western” targets, such as tourist centers in Bali, appears to be divergent
from increasing focus in 2005 on internal domestic strife in the Malukus by other
extremists with a more domestic focused agenda.
Analysts have highlighted the importance of understanding how Jihad networks
are changing. These networks increasingly depend on personal contacts and are
focused on inter-communal strife in the Mulukus and particularly in Poso which
reportedly have involved elements of JI as well as offshoots of Darul Islam and
Kompak. This is because many of the militants see this as the most likely site from
which an enclave can be carved out where Islamists can live by their interpretation
of Islamic principles. This they reportedly believe can then serve as a “building block
of an Islamic state.”49 The increased militant activity in Maluku and Posos in 2005

43 (...continued)
Press Briefing,” January 4, 2006. Eric John, “U.S. and RI: A Strategic Partnership,” The
Jakarta Post, January 3, 2006.
44 Simon Elegant Zamira, “A Killer’s Last Stand,” Time International Asia, November 21,


45 Raymond Boner, “A Sigh of Relief in Indonesia as Top Bombmaker had Taunted Police,”
The New York Times, November 11, 2005.
46 “Noordin’s Followers Still Hunted,” Media Indonesia, January 20, 2006.
47 Christopher Torchia, “Terror Expert Says JI Split into Bombing Faction and Mainstream,”
48 “Hunt for Malaysian Militant Continuing,” Agence France Presse, February 15, 2006.
49 “Weakening Indonesia’s Mujahidin Networks: Lessons from Maluku and Poso,”
International Crisis Group, October 13, 2005.

appears to be more directly linked to local dynamics, with future objectives at the
state and possibly regional level, rather than to global Jihad.50
Indonesia moved in 2005 to better utilize the resources of the TNI in the war
against violent extremists. The government has requested that the TNI revive its
Babinsa community-based military intelligence network in the territorial command
structure to assist in the war against terror. Defense Minister Juwono Sudarsono
stated that this network will serve as the “eyes and ears” of the government. Such
activities are reportedly to be coordinated by the Coordinating Minister for Political,
Legal, and Security Affairs.51 There is some concern that this activity could infringe
on individual’s rights as the network was used to quell dissent during the
authoritarian rule of former President Suharto.52 There were also calls in February
2006 for the establishment of better anti-terror laws and special courts to deal with
the terrorist threat.53 There were also signs in late 2005 that mainstream Muslim
organizations, such as Nahdlatul Ulama and Muhamediya, which together represent
some 70 million Indonesians, were increasingly willing to engage in a “war of ideas”
to counter radical Islamist ideology.54
There were two key irritants in the area of bilateral counter terror cooperation
between the United States and Indonesia in 2005. Indonesia was reportedly angry
with the United States for not informing Indonesia of the July 2005 escape of Omar
Al Farouq, who was al Qaeda’s chief operative in Southeast Asia, from Bagram air
base in Afghanistan.55 His escape was reported by the media in November, 2005.
Indonesia was also displeased that Indonesian terrorist and an Al Qaeda leader in
Southeast Asia Hambali was not released by the United States to Indonesian
custody.56 President George W. Bush has reportedly promised to return Hambali to
Indonesia once American investigators have completed their interrogation of
Hambali. Indonesia had made the case that it needs Hambali to provide evidence to
prosecute other terrorists. One possible explanation for U.S. reluctance to hand over
Hambali is the light sentence given to Baasyir.57 Yudhoyono reportedly favors
strengthening the legal system and coordination in law enforcement as well as

50 Sydney Jones, “Asking the Right Questions to Fight Terror,” The Jakarta Post, January

9, 2006.

51 “Indonesia Reactivates Military Intelligence Network,” BBC News, October 25, 2006 and
“Indonesian President Urges Army to Help Prevent Terrorism,” BBC News, October 5, 2005.
52 “Indonesia’s Military Backs Anti-terror Spy Plan,” Reuters, June 10, 2005.
53 “Overhaul of Anti-terror Laws Needed,” Dowjones Newswire, February 10, 2006.
54 Dean Yates, “Indonesian Clerics to Fight Militants in War of Ideas,” Reuters, November

21, 2005.

55 Andrew Burrell, “Terrorist Leader’s Escape Strains US-Indonesia Ties,” Financial
Review, November 4, 2005.
56 Raymond Bonner, “US Anti-Terrorism Envoy Challenged in Indonesia,” International
Herald Tribune, October 19, 2005.
57 “Jakarta to Press US For News About Hambali,” The Straits Times, January 7, 2006.

addressing the underlying economic and social forces that contribute to terrorism as
a way of dealing with the threat.58
Background. Indonesia’s attractiveness to Islamic terrorist groups appears to
derive primarily from relatively weak central government control and considerable
social and political instability and its overwhelmingly Muslim population. Central
government control in Indonesia was weakened by the 1997-99 Asian financial crisis
and the replacement of the authoritarian regime of President Suharto in 1998, which
had been in power since 1965, with a more democratic but weaker central
government. Indonesia’s former President Megawati, who was under pressure from
Islamic political parties, condemned anti-American violence and pledged to protect
U.S. assets and citizens but also publicly opposed the U.S.-led military campaigns59
in Afghanistan and Iraq. The election of Susilo Bambang Yudhoyono in 2004
raised hopes that the Indonesian central government would be both more assertive
and more effective in its counterterrorist activities. Muslim-Christian strife in the
country’s remote regions has attracted the involvement of foreign Islamic radicals,
including, apparently, some with Al Qaeda connections.
Although the overwhelming majority of Muslim Indonesians follow a moderate
form of Islam, fundamentalist Islamic theology is growing in popularity in Indonesia,
and radical groups have grown in influence by taking advantage of the country’s
internal problems. These include separatist movements, a severe economic recession
following the Asian financial crisis, problems associated with the evolving reform
process and clashes between Christians and Muslims. Radical groups such as Laskar
Jihad and the Islamic Defenders Front also reportedly have received assistance from
elements within the Indonesian military (TNI) in organizing, securing arms, and60
transport to locales throughout the Indonesian archipelago.
Even the more extreme groups traditionally have been concerned primarily with
domestic issues such as promoting the adoption of Islamic law (sharia). In the 1999
national elections, only a small minority of the Muslim parties favored radical
Islamic agendas, and overall the Muslim parties drew less than one-fifth of the vote.
More recently, however, the U.S.-led campaign against terrorism and war in Iraq
have had negative political resonance with a variety of groups currently jockeying for
power and influence. Former President Megawati reportedly feared cooperating too
closely with U.S. demands for arrests and other measures could leave her vulnerable
to political attack not only by radical Islamists, but perhaps more importantly, by
secular nationalists.61

58 Donald Greenless and John McBeth, “Terrorists New Tactic: Assassination,” The Far
Eastern Economic Review, June 17, 2004.
59 Richard Paddock, “Indonesia Presses U.S. to Stop Bombing Asia,” Los Angeles Times,
November 2, 2001.
60 “Al-Qaida Planned Indonesia Attack,” Associated Press, January 23, 2002. This report
cites Indonesian military sources and western intelligence sources that the Indonesian army
committed at least $9.3 million to finance Laskar Jihad.
61 December 2002 conversation with Zachary Abuza.

Jakarta’s Counter-Terrorism Policy. Until Indonesia’s policy reversal
following the October 2002 Bali bombing, U.S., Singaporean, and Malaysian
officials expressed dissatisfaction with the level of Indonesia’s cooperation against
terrorism. The first Bali attack spurred Indonesia to take the terrorism threat more
seriously. Jemaah Islamiyah’s killing of Indonesian civilians was likely a key factor
in the Indonesian government’s decision to take a much stronger stand and cooperate
with U.S. authorities, despite a marked fall in Indonesians’ favorable impressions of
the United States (discussed below). In addition, the trial of Baasyir brought much
evidence of terrorist activities to light, bringing home the extent of the terrorist threat
in Indonesia. The danger was highlighted in July 2003 by the J.W. Marriott
bombing, which was preceded by several arrests, including an Indonesian police raid
that uncovered a possible JI assassination plot of four members of the Peoples62
Representative Council (DPR). The limits of the government’s commitment to
prosecuting the war on terror in an election year were demonstrated by the reduction
of Baasyir’s sentence. Mitigating against backtracking by the government on its
counterterror stance is Indonesia’s need for foreign investment from abroad and the
perception that Islamist extremists are a threat to the nationalists’ political position.
President Bush’s three-hour visit to Bali on October 22, 2003, was designed to
strengthen bilateral counterterror ties. In a joint statement, President Bush and
President Megawati pledged “to enhance their bilateral cooperation in the fight
against terrorism, including through capacity building and sharing of information,”63
specifically referring to military-to-military relations The United States and
Indonesia presently cooperate on counterterrorism in a number of areas with
assistance going to the police and security officials, prosecutors, legislators,
immigration officials, banking regulators and others. U.S. - Indonesian counterterror
capacity building programs have included funding for the establishment of a national
police counterterrorism unit, counterterrorism training for police and security
officials, financial intelligence unit training to strengthen anti-money laundering,
train counterterror intelligence analysts, and an analyst exchange program with the
Treasury Department. Other programs include training and assistance to establish a
border security system as part of the Terrorist Interdiction Program; and regional
counterterrorism fellowships to provide training on counterterrorism and related
issues to the Indonesian military.64
The United States’ popularity amongst Indonesians has dropped significantly
in recent years. According to polling data, 79% of Indonesians had a favorable
opinion of the United States in 1999, 61% did in 2002, and only 15% did in 2003.65

62 “A Number of Pesantrens in Central Java Targets,” Jakarta Suara Pembaruan, July 16,

2003, FBIS.

63 “Joint Statement Between the United States of America and the Republic of Indonesia,”
The White House, October 22, 2003.
64 Information drawn from State Department Fact Sheet “Summary of Counter Terrorism
Assistance for Indonesia,” 10/03 update.
65 See Dan Gardner, “Bush is Losing the War for Hearts and Minds,” The Ottawa Citizen,
March 13, 2004 and Ellen Nakashima, “U.S. Policy Censured in Indonesia,” The

Another poll stated that 83% of Indonesians took an unfavorable view of the United
States in 2003.66 A more recent Center for Strategic and International Studies (CSIS)
report found that “Sustained resentment of the United States and its policies, if left
unchecked, undermines prospects for building and maintaining cooperation between
the United States and Indonesia in countering the influence of extremist and violent
groups in Indonesia and promoting democracy and stability in Southeast Asia.”67 It
is thought that American post-tsunami assistance in 2005/2006 has done much to
improve Indonesians’ perceptions of the United States. Some Indonesian analysts
view the United States as focused on the “search and destroy” aspect of the war
against terror and feel that the United States has not focused sufficient attention to
winning the “hearts and minds” aspect of the struggle, particularly in regard to U.S.
policy towards the Israel-Palestinian issue.68
In 2004 Indonesia focused on a series of elections that led to only limited gains
by Islam-based parties. With 33.57% of the vote, Democratic Party leader Susilo
Bambang Yudhoyono, a retired general and former Security Minister, and his running
mate Jusuf Kalla, received more votes than any other candidate in the first round of
the presidential election.69 A final round between Yudhoyono and former President
Megawati Sukarnoputri of the Indonesian Democratic Party of Struggle (PDI-P), who
polled 26.61% of the vote in the first round, held on September 20, 2004, led to
Yudhoyono’s victory. In the election, Islam-based parties increased their appeal
among Indonesian voters from 16% in the 1999 election to 21.34% in the 2004
election.70 They did this in part by downplaying their overtly Islamist message and
instead focusing on anti-corruption and good governance.
The Philippines
The Philippines condemned the September 11, 2001 attacks and offered ports
and airports for use by U.S. naval vessels and military aircraft for refueling stops.
Philippine President Gloria Macapagal-Arroyo and President Bush agreed on the
deployment of U.S. military personnel to the southern Philippines to train and assist
the Philippine military against the terrorist Abu Sayyaf group.
The 2002 Balikatan Operation on Basilan Island. The number of
American military personnel deployed between January 2002 and July 31, 2002 was

1,300, including 160 Special Forces. The exercise, dubbed “Balikatan” or “shoulder-

65 (...continued)
Washington Post, October 21, 2003.
66 Tom Plate, “What if Bush Were to Face an Election in Asia,” Straits Times, January 19,


67 Lena Kay, “Indonesian Public Perceptions of the U.S. and Their Implications for U.S.
Foreign Policy,” Pacific Forum, Center for Strategic and International Studies, August 2005.
68 Philips Jusario Vermonte, “Coordination Needed to Fight Terrorism,” Center for Strategic
and International Studies-Jakarta, February 12, 2004.
69 “Presidential Election First Round Results,” U.S.-Indonesia Society, August 5, 2004.
70 Greg Fealy, “The 2004 Indonesian Elections,” Australian National University, data sheet.

to-shoulder,” included the deployment of over 300 troops, primarily Navy engineers,
to the Southern Philippines to undertake “civic action” projects such as road-building
on Basilan, an island that had been a center of Abu Sayyaf’s activities. The U.S.
military role was designated as non-combat. The Balikatan exercise reportedly
resulted in a significant diminishing of Abu Sayyaf strength on Basilan. Armed
Forces of the Philippines (AFP) operations improved as a result of U.S. assistance
in intelligence gathering, the supplying of modern equipment, and aid in the planning
of operations.71
The Abu Sayyaf Group. Abu Sayyaf is a small, violent, faction-ridden
Muslim group that operates in the western fringes of the big island of Mindanao and
on the Sulu islands extending from Mindanao. It has a record of killings and
kidnappings and has had links with Al Qaeda. Abu Sayyaf kidnapped three
American citizens in May 2001. One was beheaded in June 2001. The other two,
a missionary couple, the Burnhams, were held by Abu Sayyaf until June 2002 when
Filipino army rangers encountered the Abu Sayyaf groups holding the Burnhams. In
the ensuing clash, Mr. Burnham and a Filipina female hostage were killed, but Mrs.
Burnham was rescued.
The Philippine-U.S. Balikatan operation and follow-up AFP operations reduced
Abu Sayyaf’s armed strength from an estimated 1,000 to 200-400, but it continued
to operate in the Sulu islands south of Basilan. Under the leadership of Khadaffy
Janjalani, Abu Sayyaf reoriented its strategy and appears to have gained greater
effectiveness as a terrorist organization. Janjalani de-emphasized kidnappings and
instead emphasized developing capabilities for urban bombings. He relocated
elements of Abu Sayyaf to the western Mindanao mainland. He improved ties with
military factions of the Moro Islamic Liberation Front (MILF) and established links
with JI. Using several MILF base camps, Abu Sayyaf and JI reportedly engage in
joint training with emphasis on training in bomb-making and planning urban
bombings.72 By mid-2005, JI personnel reportedly had trained about 60 Abu Sayyaf73
cadre in bomb assembling and detonations. Since 2003, Abu has carried out
bombings and plotted bombings in cooperation with JI and the MILF, including
bombings in Manila. Abu Sayyaf also has operated with the Rajah Solaiman
Movement, a group of Filipino Muslim converts from the Manila area.
The MILF. The U.S. focus on Abu Sayyaf is complicated by the broader
Muslim issue in the southern Philippines, including the existence of a larger
insurgent-terrorist group, the Moro Islamic Liberation Front (MILF). The MILF,
with an estimated armed strength of 10,000-12,000, broke away from another
Muslim group, the Moro National Liberation Front (MNLF) in the late 1970s. It

71 Gloria, Glenda M. “Training days.” Manila Newsbreak (Internet version), July 8, 2002.
Schmitt, Eric. By aiding needy Filipinos, G.I.’s could help rout the rebels. New York Times,
June 15, 2002. p. A6.
72 Abuza, Zachary. Balik-Terrorism: The Return of the Abu Sayyaf. Carlisle, U.S. Army
War College, 2005, p. 27.
73 Mogato, Manny. Philippine rebels linking up with foreign jihadists. Reuters News,
August 21, 2005. Del Puerto, Luige A. PNP [Philippine National Police]: Alliance of JI,
RP terrorists strong. Philippine Daily Inquirer (internet version), November 20, 2005.

seeks independence for the Muslim region of the southern Philippines. Its main
political objective has been separation and independence for the Muslim region of
the southern Philippines. Evidence, including the testimonies of captured Jemaah
Islamiyah leaders, has pointed to strong links between the MILF and JI, including the
continued training of JI terrorists in MILF camps and the planning of terrorist
operations. This training appears to be important to Jemaah Islamiyah’s ability to
replenish its ranks following arrests of nearly 500 cadre in Indonesia, Malaysia, and
Singapore.74 MILF leaders deny links with JI; but here are many reports linking MILF
base commands with the terrorist organization. A stronger collaborative relationship
has developed between MILF commands and Abu Sayyaf since 2002, according to
Zachary Abuza, a U.S. expert on Islamic terrorism in Southeast Asia.75
The MILF has had tenuous cease-fire agreements with the Philippine
government. The government and the MILF concluded a new truce agreement in
June 2003. There has been a substantial reduction in violence and armed clashes
under the truce. A team of international observers began to monitor the cease-fire in
October 2004. A new round of Philippine government-MILF political talks began
in early 2005, and the both sides have predicted an agreement in the first half of
2006. However, the collaboration between several MILF base commands with JI and
Abu Sayyaf indicate that key elements of the MILF would not support any agreement
that did not include outright independence for the Muslim areas.
The Philippine Communist Party (CPP). The CPP, the political head of
the New Peoples Army (NPA), also has called for attacks on American targets. The
Bush Administration placed the CPP and the NPA on the official U.S. list of terrorist
organizations in August 2002. It also pressured the government of the Netherlands
to revoke the visa privileges of Communist Party leader, Jose Maria Sison, and other
CPP officials who have lived in the Netherlands for a number of years and reportedly
direct CPP/NPA operations. In December 2005, the European Union placed the
CPP/NPA on its list of terrorist organizations.
Subsequent Military Operations and Controversies over the U.S.
Role. The United States and the Philippines have attempted to negotiate a second
phase of U.S. training and support of the AFP since late 2002. The negotiations have
experienced difficulties in determining the “rules of engagement” for U.S. personnel
and the terminology to be used in describing Philippine-U.S. cooperation. The basic
issue has been whether any facets of the U.S. role could be considered a combat role.
In late 2002, two sides announced that U.S. training of AFP light reaction companies
would take place in northern Luzon and again on Mindanao. This program has been
ongoing. The objective was to train 16 light infantry companies by the end of 2003
for use against both Muslim insurgents and the NPA. However, Filipino political
opposition arose when a U.S.-Philippine agreement was disclosed in early 2003 for
a U.S. military role against Abu Sayyaf on Jolo island that was larger in numbers and
appeared to include a combat role for U.S. military personnel. The Bush and Arroyo
administrations decided to put the plan on hold and re-negotiate.

74 John McBeth, “Across Borders,” Far Eastern Economic Review, July 22, 2004. p. 27.
75 Abuza, Balik-Terrorism: The Return of the Abu Sayyaf, p. 14-19, 22-24.

The result was agreement for two operations in 2005 and into 2006. One
focused on Abu Sayyaf on western Mindanao, undoubtedly in response to Khadaffy
Janjalani’s shift of Abu Sayyaf operations to the Mindanao mainland. The second
focused on Jolo but with a reduced, non-combat U.S. military role as compared to
the plan of 2003. (For details of the U.S. military roles, see The Republic of the
Philippines: Background and U.S. Relations. CRS Report RL33233. And Abu
Sayyaf: Target of Philippine-U.S. Anti-Terrorism Cooperation. CRS Report
RL31265.) The operations apparently have had three objectives: (1) neutralize Abu
Sayyaf-JI training; (2) kill or capture Khaddafy Janjalani and other Abu Sayyaf
leaders; and (3) root out the Abu Sayyaf forces and organization on Jolo in a similar
fashion to the success on Basilan in 2002.
Violence Continues in Southern Provinces. Since January 2004,
sectarian violence between insurgents and security forces in Thailand’s majority-
Muslim provinces has left over1,000 people dead at a rate of about 50 killed per
month. The toll includes suspected insurgents killed by security forces, as well as
victims of the insurgents: both Buddhist Thais, particularly monks and teachers, and
local Muslims. According to a Thai police report, 70% of the victims were
civilians.76 The southern region, which includes the provinces of Yala, Narathiwat,
Pattani, and Songhkla, has a history of separatist violence, though the major
movements were thought to have died out in the early 1990s. Thai Muslims have
long expressed grievances for being marginalized and discriminated against, and the
area has lagged behind the rest of Thailand in economic development.
After a series of apparently coordinated attacks in early 2004, the central
government declared martial law in the region. A pattern of insurgent attacks —
targeted shootings or small bombs that claim a few victims at a time — and counter-
attacks by the security forces has developed. The pattern crystallized into two major
outbreaks of violence in 2004: on April 28, Thai soldiers killed 108 insurgents,
including 34 lightly armed gunmen in a historic mosque, after they attempted to
storm several military and police outposts in coordinated attacks; and, on October 25,
84 local Muslims were killed: 6 shot during an erupting demonstration at the Tak Bai
police station and 78 apparently asphyxiated from being piled into trucks after their77
arrest. The insurgents retaliated with a series of more gruesome killings, including
beheadings, following the Tak Bai incident. Facing a trend of more sophisticated and
coordinated attacks, observers note that such confrontations have led to an increasing
climate of fear and division along religious lines.78

76 According to the report, at the end of 2005, the death toll included 1,069 civilians, 191
militants, 90 police, and 33 soldiers. Source: Agence Prance Presse. January 4, 2006.
77 Independent forensic experts said that the men died piled on top of each other with their
hands tied behind their backs. See Mydans, Seth, “Thai King Urges Premier to Be More
Lenient in the Muslim South,” New York Times, Nov. 2, 2004.
78 Chulalongkorn University professor Panitan Wattanyagorn, quoted in Christian Science
Monitor. July 20, 2005.

Central Government Response. The number of security forces on the
ground has steadily increased, from an initial dispatch of 3,000 troops to over 11,00079
soldiers and nearly 20,000 police by late 2005. In July 2005, Thaksin announced
the lifting of martial law but replaced it with a new emergency decree allowing him
to assume emergency powers, including authority to grant immunity to security
officials, hold suspects without charge for up to 30 days, and a variety of other80
extraordinary measures that critics say impinge on civil liberties. The measure was
passed and later renewed by the Parliament. Since then, the Thaksin Administration
has set aside $16 million to purchase thousands of new M16 rifles for use by military
personnel in the region.81
Additional units of police officers were sent in early 2006 to increase the arrest
rate of suspected insurgents. According to the police, 100 were arrested in the
second half of 2005,82 but sources say that police were not able to identify suspects83
in over 85% of violent incidents. Reflecting a belief that the violence is being
fomented in madrassas with foreign links, police have arrested several Indonesia-
educated teachers in the Islamic schools. Controversial tactics have included the
designation of suspected separatist areas as “red zones,” a designation that denies
funding for local development, and the use of blacklists to compel suspected
militants to attend “re-education” programs. Critics contend that the lists are based
on weak intelligence and little hard evidence. There have been several unconfirmed
reports of extra-judicial killings.84
In addition to the sizable military dispatch, Thaksin has adopted measures
designed to soften criticism that his policy overly stressed the use of military force.
The government has proposed aid packages to the south and pledged to reform the
Islamic school system. After public outcry over the deaths of Muslim youths by Thai
troops, government-commissioned independent investigations of the April and
October 2004 incidents led to the dismissal or reassignment of some officials, but
largely acquitted the security forces of any intentional misconduct. The Thaksin
Administration approved a $500 million economic development program for the
region, although local sources complain that the funds are slow to be disbursed. In
March 2005, the government created the National Reconciliation Commission
(NRC), headed by former prime minister Anand Panyarachun, to address the
violence. The NRC recommended lifting martial law and criticized the executive
decree as ineffective.85

79 “Politics: Vicious Circle,” Economist Intelligence Unit. November 14, 2005.
80 “Thai Teachers Become Targets in the South,” Washington Post. August 12, 2005.
81 “Politics: Vicious Circle,” Economist Intelligence Unit. November 14, 2005.
82 “Thailand to Send Another 5,300 Police to Restive South,” AFX Asia. January 1, 2006.
83 “Thailand’s Emergency Decree: No Solution,” International Crisis Group Report.
November 18, 2005.
84 Ibid.
85 “Draconian Powers for Thaksin,” Economist Intelligence Unit - Business Asia. July 25,


Criticism of Thaksin’s Approach. The government’s handling of the
violence has been widely criticized as ineffective and inflammatory. Critics charge
that the Thaksin Administration has yet to put forth a sustained strategy to define and
address the problem, has repeatedly but arbitrarily shuffled leadership positions of
those charged with overseeing the region, and has failed to implement adequate
coordination between the many security and intelligence services on the ground.86
Further, measures under the emergency decree and the failure to stop the bloodshed
has bolstered local suspicion of the security forces. Some maintain that such distrust
has led to local cooperation with the militants, a claim reinforced by a reported
incident in September 2005 in which outside militants killed two Thai marines who
had been taken hostage by a group of angry villagers.
Parties outside of the Administration have expressed concern about the
government response. The royal family, which commands strong loyalty from the
Thai public, has taken the unusual step of publicly intervening. In a move that may
have forced Thaksin to soften his statements, King Bhumibol Adulyadej publicly
encouraged him to take a more measured approach. Dissent has emerged from
within the elite as well: a former prime minister and ex-Army chief have harshly87
criticized the use of force. The chairman of the NRC claimed that the emergency
decree provided a “license to kill” for security forces.88 Opposition parliamentarians
and academics have also spoken out, but overall public support for Thaksin’s
approach remains high; 72% of respondents supported the emergency decree in a July89

2005 poll.

Multiple international human rights groups have expressed concern about
Thaksin’s handling of the situation. A January 2006 report by Amnesty International
accused the government of unlawful methods, including “arbitrary arrest and
detention procedures; torture and ill-treatment of those arrested in relation to the
violence; failure to investigate killings and possible ‘disappearances’; and impunity
of the security forces under the provisions of the 2005 Emergency Decree.”90 Human
Rights Watch condemned the reported use of “blacklists” of suspected militants to
force individuals to attend “re-education camps.” 91
Degree of Foreign Involvement Uncertain. Many experts characterize
the movement as a confluence of different groups: local separatists, Islamic radicals,
organized crime, and corrupt police forces. They stress, however, that sectarian

86 See “Southern Thailand: Insurgency, Not Jihad,” International Crisis Group Asia Report.
May 18, 2005.
87 “Anand, Surayud Urge Peaceful Resolution,” The Nation (Bangkok), Nov. 16, 2004.
88 “Thailand’s Emergency Decree: No Solution,” International Crisis Group Report.
November 18, 2005.
89 Ibid.
90 “If You Want Peace, Work for Justice,” Amnesty International Report. January 4, 2006.
Accessed at: http://web.amnesty.org/library/Index/ENGASA390012006
91 “Thailand: Blacklists Create Climate of Fear,” Human Rights Watch News. December 17,
2005. Accessed at http://hrw.org/english/docs/2005/12/16/thaila12317.htm

violence involving local Muslim grievances provides a ripe environment for foreign
groups to become more engaged in the struggle. Such experts have warned that
outside groups, including JI and other militant Indonesia-based groups, may attempt
to exploit public outrage with events like the October 2004 deaths to forge alliances
between local separatists and regional Islamic militants.92 Pictures of Muslim
casualties after the 2004 incidents were posted on an Al Qaeda website in an apparent
attempt to exploit the conflict. Some analysts believe that the heavy-handed response
by the Thai security forces, with the open support of Thaksin, has swayed public
opinion of the southern population to support the movement.
Organizations such as Pulo (the Pattani United Liberation Organization), BRN
(the Barisan Revolusi Nasional), and GMIP (Gerakan Mujahadeen Islam Pattani),
earlier assumed to be defunct, were linked to JI in the past. An organization called
“Bersatu” claims to be an umbrella grouping for all the insurgent factions, but
appears to have very limited authority over the disparate networks.93 Some experts
say that an evolving sense of pan-national Islamic identity could shift the focus of the
movement in the South from local autonomy to international jihadism. In addition,
separatist groups in the region have reportedly received financial support from groups
in other Islamic countries, and some of the leaders trained in camps in Libya and
Thailand as a Convenient Base. In addition to indigenous violence,
confessions of detained Al Qaeda and JI suspects indicate that the groups have used
Thailand as a base for holding meetings, setting up escape routes, acquiring arms,95
and laundering money. There are indications of JI presence in Thailand, particularly
given the 2003 arrests of Hambali, a radical figure with suspected ties to Al Qaeda,
and of three Islamic leaders suspected of planning to attack foreign embassies and
tourist destinations. In January 2002, Hambali is reported to have convened a
meeting of JI’s operatives in southern Thailand at which the group agreed to attack
“softer” targets. A number of Al Qaeda and JI figures, including convicted World
Trade Center bomber Ramzi Yousef, have taken advantage of lax border controls and
tourist-friendly visa requirements to flee to Thailand to escape arrest in other96
Southeast Asian countries.
Impact on Regional Relations. Thailand’s neighbors have expressed alarm
at the continuing insurgency in the South, breaking the ASEAN rule of broaching

92 “Thailand ‘The Next Battleground,” The Australian. December 1, 2004.
93 “Thai Separatists Leader Reaches Out for Talks with Government,” Xinhuanet. May 22,


94 Ibid.
95 Regional terrorism experts have pointed to linkages to JI in Thailand through the group
Jemaah Salafi, which reportedly had contact with Hambali as he was planning major
bombings in Bangkok; through personal ties with various secessionist leaders; and through
the participation in the attacks of several foreign nations with JI ties.
96 Western intelligence sources reportedly estimate that Thai immigration authorities detain
on average one person a day, usually from South Asia, for traveling with forged documents.
“Canada Helps Thais Combat Terror,” Far Eastern Economic Review. September 19, 2002.

internal affairs at the November 2004 ASEAN summit in Laos. Although Thaksin
resisted attempts to add the discussion to the official agenda, Indonesia and
Malaysian leaders met with him on the sidelines to convey their concern. Australian
Foreign Minister Alexander Downer has noted the mishandling and pointed out the
potential for JI to exploit local grievances.97 The U.S. State Department also has
acknowledged its concern and intent to monitor the situation closely.98
The violence has particularly hurt relations between Thailand and Malaysia.
Many of the Muslim Thais are ethnically Malay and speak Yawi, a Malay dialect.
Relations with Malaysia were particularly strained after over 130 Thai Muslims fled
across the border into Malaysia in September 2005, seeking asylum and claiming
persecution by Thai security forces. Bangkok has demanded their repatriation, but
Malaysia instead engaged the United Nations to determine the individuals’ refugee
status. The Malaysian public has grown increasingly angry at the perceived violence
against Muslims in Thailand. This downturn in bilateral relations followed some
progress in cross-border cooperation since the violence began: Malaysia had pledged
more troops and equipment to increase border security, conducted joint border patrols
with Thai counterparts, and agreed to terminate the joint citizenship privileges that
some believe facilitate the passage of terrorists across the border.
A New Front in the War on Terror? Some observers have speculated that
if the insurgency spreads, southern Thailand may become another front on the U.S.-
led war on terrorism in Southeast Asia. Thailand and the United States have close
anti-terrorism cooperation, institutionalized in the joint Counter Terrorism
Intelligence Center (CTIC), which was reportedly established in early 2001 to
provide better coordination among Thailand’s three main security agencies. The U.S.
Central Intelligence Agency reportedly shares facilities and information daily in one
of the closest bilateral intelligence relationships in the region. The CIA reportedly has
assigned approximately 20 agents to the CTIC and in 2002 provided between $10
million and $15 million to the center. According to press reports, the CTIC took the
lead in capturing Hambali and also has captured a number of other suspected JI99
operatives, acting on CIA intelligence. Thailand reportedly also provided a “black
site” where U.S. Central Intelligence Agency officials were allowed to secretly hold
suspected terrorists. According to press reports, two major Al Qaeda figures
captured in Pakistan were flown to Thailand for interrogation by U.S. officials.100

97 “Tackling the Thai Terror Threat,” Asian Wall Street Journal. November 30, 2004.
98 State Department Press Releases and Documents, October 29, 2004.
99 Shawn W. Crispin and Leslie Lopez, “A Thai-CIA Antiterrorism Team,” Wall Street
Journal. October 1, 2003.
100 “CIA Operates Secret Prisons Outside U.S.,” Wall Street Journal Asia. November 2,


President Bush designated Thailand as a major non-NATO ally101 in 2003 in
recognition of its support of the war against terrorism.
In 2005, Prime Minister Abdullah Badawi urged Muslims around the world to
guard against extremism and improve ties with the West while promoting his102
nation’s moderate version of Islam known as Islam Hadhari or Civilizational Islam.
According to Deputy Secretary of State Robert Zoellick the United States remained103
confident in Malaysia’s ability to handle the threat of terrorism. There has also
been some concern that insurgents in Thailand’s Muslim south may have received
support from individuals across the border in Malaysia though the Malaysian
government has not been involved.104 Malaysia, Singapore, Thailand and Indonesia
also made progress in addressing potential terrorist and pirate threats to the maritime
shipping lanes in the straits of Malacca in 2005 by agreeing on operating procedures
that will allow patrols of each state to enter into the territorial waters of others when
in pursuit of pirates or terrorists.105 In January 2006, Prime Minister Abdullah Badawi
and President Susilo Bambang Yudhoyono met in Sumatra where they discussed
ways to enhance counter terror information exchange among other issues.106
As mentioned above, for a period in the late 1990s, Malaysia was the locus of
JI’s and Al Qaeda activity. In 1999 and 2000, several Al Qaeda operatives involved
in the September 11 and the USS Cole attacks used Kuala Lumpur as a meeting and
staging ground. According to the confessions of one captured Al Qaeda leader,
Malaysia was viewed as an ideal location for transiting and meeting because it107
allowed visa-free entry to citizens of most Gulf states, including Saudi Arabia.
Malaysia’s former Prime Minister Mahathir Mohammed, a longstanding
promoter of non-violent Muslim causes, openly criticized Islamic terrorists after
September 11, including Palestinian suicide bombers. In a show of appreciation for
his cooperation, Mahathir was invited to Washington, D.C., and met with President
Bush in mid-May 2002. During that visit the United States and Malaysia signed a

101 Under section 517 of the Foreign Assistance Act of 1961, the President can designate a
non-North Atlantic Treaty Organization state as a major ally for the purposes of the Foreign
Assistance Act and the Arms Export Control Act. The designation allows states more access
to U.S. foreign aid and military assistance, including weapons purchases and development.
102 “Malaysia PM Abdullah Warns Muslims Against Extremism,” Voice of America, January

27, 2005.

103 “Malaysia’s Efforts Against Terrorism,” Bernama, June 8, 2005.
104 “Analyst Says Malaysia not Involved in Southern Thailand Unrest,” BBC News, January

12, 2006.

105 Michael Richardson, “Maintaining Security in Malacca Strait,” The Jakarta Post, January

11, 2006.

106 Joko Hariyanto, “Indonesia, Malaysia Leaders Discuss Terrorism, Sensitive Border
Areas,” Associated Press, January 12, 2006.
107 The 9/11 Commission Report, p. 158.

Memorandum of Understanding (MOU) on counter-terrorism. The text of that
document became the basis for a subsequent declaration on counter-terrorism that the
United States and ASEAN signed at the August 2002 ASEAN Regional Forum
(ARF) meeting.108
The Bush Administration also has decided to downplay U.S. human rights
concerns over Malaysia’s use of its Internal Security Act (ISA) to imprison political
opponents without trial, especially since Kuala Lumpur has employed the ISA against
suspected members of JI and the Kampulan Mujiheddin Malaysia (KMM).109
Mahathir’s successful visit to Washington, DC, in May 2002 symbolized the
fundamental change in the U.S. posture toward him since the September 11 attack.
However, Mahathir criticized the U.S. attack on Iraq and new U.S. visa restrictions
on Malaysians seeking to enter the United States.
Shortly after taking office in the fall of 2003, Malaysia’s new Prime Minister
Abdullah Ahmad Badawi pledged to continue Malaysian support for the war against
terror.110 In March 2004, Badawi’s National Front Coalition won a significant victory
over Malaysian Islamists who favor an extreme form of Islam. During the February
Counterterrorism conference in Bali, it was reported that Attorney General Ashcroft
complimented Malaysia for its anti-terrorism efforts and for progress made on a
Mutual Legal Assistance Treaty (MLAT).111 In a statement before the Organization
of Islamic Conference (OIC) Prime Minister Abdullah Badawi reportedly called on
the United States to change its foreign policy to counter the perception, held by many
in the Islamic world, that it is anti-Islamic.112

108 U.S. Embassy, Malaysia, Speech by U.S. Ambassador Marie T. Huhta, Rotary
International Dinner Forum, Kuala Lumpur, Malaysia February 22, 2003.
[http://usembassymalays ia.org.my/ams p0222.html ].
109 The KMM is a small, militant group calling for the overthrow of the Malaysian
government and the creation of a pan-Islamic state encompassing Malaysia, Indonesia, and
the southern Philippines. Founded in 1995, the group is estimated by Malaysian authorities
to have fewer than 100 members. According to Singaporean and Malaysian authorities, the
KMM has close links to JI and radical Islamist groups in the Malukus and the Philippines.
U.S. State Department, Patterns of Global Terrorism 2001, p. 123-24,
[http://www.state.gov/s/ct/rls/pgtrpt/]. The KMM’s links to Malaysia’s main opposition
party, Parti Islam se-Malaysia (PAS), are controversial. After the September 11, 2001
attacks, Prime Minister Mahathir explicitly linked PAS to the KMM and international
terrorist movements, and went on a political offensive against the party, which had made
gains in recent local elections. Several of the alleged KMM members arrested are allegedly
PAS members, including some senior party leaders. Abuza, “Tentacles of Terror,” February

5, 2003 draft, p. 40.

110 “Malaysia Pledges Terror Fight,” The Wall Street Journal, November 4, 2004.
111 The MLAT will establish cooperation for the prosecution of terrorist suspects in both
countries. It will also assist in the exchange of witnesses and in terrorist investigations.
“U.S. Compliments Malaysia for Role in Anti-terror Efforts,” Bernama Daily, February 5,


112 “Time For US to Change its Image,” Today, January 28, 2005.

Mainstream Islam in Malaysia appears to have reasserted its moderate character.
Though the late 1990s saw a significant electoral swing toward the radical Islamist
party, Parti Islam se-Malaysia (PAS), parliamentary elections in March 2004
significantly rolled back PAS’ earlier gains. Badawi’s Barisan National (BN) party
polled 64.4% of the vote and took 196 out of 219 seats in parliament.113 PAS lost
control of Terengganu and only just held on to Kelantan leaving it in control of only
one of 13 state governments with BN controlling the rest. PAS seats in parliament
fell from 26 seats to seven. The election result is interpreted as a sign that Malaysians
are comfortable with Badawi. It is also seen as demonstrating the limited appeal of
radical Islamic policies espoused by PAS.114
Recent Developments. Malaysia’s Prime Minister Datuk Seri Abdullah
Badawi reportedly sought to strengthen bilateral ties with the United States during
his July 2004 meeting with President Bush in Washington, DC.115 Although not
uncritical of the United States policies, such as the Israel/Palestinian issue, Badawi
is a moderate Islamic leader that is giving indications that Malaysia will continue to116
be a valuable partner in the war against terror in Southeast Asia. Badawi has urged
that the war on terror take into account the root causes of terror and has warned that
if it does not “for every one we kill, five more will emerge to continue their
struggle.”117 An NGO coalition in Malaysia known as Peace Malaysia headed by the
son of former Prime Minister Mahathir Mohammad ran a series of television
advertisements in January 2005 that denounced terrorism as un-Islamic stating that118
“violence dishonors faith.”
The threat of seaborne terrorism in the region, particularly in the vital Straits of
Malacca between Malaysia and Indonesia, has received increased attention. Admiral
Thomas Fargo visited Malaysia to coordinate sharing of intelligence and to offer to
help build the capacity of Malaysia, and other regional countries, to deal with such119
a threat. Fargo reportedly initially displeased Malaysia and other regional states
when he mentioned, in response to a question during congressional testimony, that

113 Malaysia Primer, Virtual Information Center, U.S. Department of Defense, April 12,


114 “Malaysia Politics: Election Winner and Losers,” Economist Intelligence Unit, March

24, 2004.

115 See CRS Report RL32129, Malaysia: Political Transition and Implications for U.S.
Policy, by Bruce Vaughn.
116 Speech by The Honorable Abdullah Badawi, Prime Minister of Malaysia, Washington,
DC, July 19, 2004.
117 “Disquiet as Bush Dominates Agernda at Asia Pacific Sumit,” Agence France Presse,
November 21, 2004.
118 “Malaysian TV Runs Anti-terror Campaign Aimed at Muslims,” Agence France Presse,
January 2005.
119 “Seaborne Terrorism is a Serious Threat: Fargo,” Agence France Presse, June 24, 2004.

the United States might consider dispatching ships to patrol the Strait rather than
assist regional states in doing so.120
Singapore has been at the forefront of anti-terrorist activity in Southeast Asia.
A terrorist attack on the city-state could jeopardize its standing as the region’s
financial and logistical hub. As recently as August 2005, some experts cited
Singapore as a possible Al Qaeda target based on its influence in the world economy
and as a strong U.S. defense partner. Under its Internal Security Act, Singapore has
arrested 37 Islamic militants. Of those, 13 are members of Jemaah Islamiah (JI), a
designated foreign terrorist organization with reported links to Al Qaeda, for
allegedly plotting to bomb the U.S. Embassy and other targets. Authorities claim that
many of the other suspects have links to the Philippines-based Moro Islamic
Liberation Front (MILF). In September 2004, Singapore announced that it had
extended by two years the detention of alleged terrorists. The government of
Singapore has outlined measures that it has taken to dismantle JI operations in
Singapore in a white paper entitled “The Jemaah Islamiah Arrests and the Threat of
Reformed Homeland Security Apparatus and Counterterror
Strategy. After 9/11, Singapore created a new body within the Prime Minister’s
office to centralize its revised security architecture: the National Security
Coordination Secretariat (NSCS) is responsible for national security planning and the
coordination of policy and intelligence. The official in charge of the NSCS reports
to the Prime Minister through the Security Policy Review Committee (SPRC), which
includes the Ministers of Defense, Home Affairs, and Foreign Affairs. In addition
to a revamped bureaucracy, Singapore has instituted a number of specific programs
to protect its homeland. Singaporean officials maintain that important port facilities
and other major targets remain vulnerable and have stepped up protection of these
and other critical infrastructure. Measures include camera surveillance of water and
power facilities, enhanced security at embassies and prominent public areas, and the
deployment of armed personnel at the major petrochemical hub on Juron Island. The
regulation of people and goods across Singapore’s borders has also been intensified
through the merging of the border control functions of the customs and immigration
services. The Joint Counter Terrorism Center (JCTC) coordinates the multiple
agencies and departments of the Singaporean government that deal with terrorism,
including the intelligence agencies.
Preparing the Public. Through its “Total Defense” campaign, which calls
on all Singaporeans to participate in the national defense, the government has been
psychologically preparing its public for an attack by framing the question of a
terrorist attack as “when, not if.” Even as Prime Minister Lee Hsien Loong
congratulated the country on strong economic growth in his New Year’s message in
2006, he warned that a terrorism remains a tremendous threat to Singapore’s
prosperity and called for further countermeasures. In January 2006, Singapore
authorities staged a large simulated emergency response drill in which the mass

120 Barry Wain, “Strait Talk,” Far Eastern Economic Review, April 22, 2004.

transit system was attacked with bombs and chemical weapons. More than 2,000
people from 22 different government agencies participated in the exercise.
Tightening Government Control. The ruling People’s Action Party (PAP)
has emphasized the terrorist threat to reinforce its ideology that the government plays
an important role in enforcing social discipline and harmony in society, even at the
expense of individual liberties. Under the Internal Security Act, the government can
prohibit or place conditions on publications that incite violence, advocate
disobedience to the law, arouse tensions among the various ethnic, religious, and
linguistic groups, or that might threaten national interests, national security, or public
order. In October 2005, a Singapore court sentenced two ethnic Chinese bloggers for
posting racist remarks about ethnic Malays, the first such prosecution under the
Sedition Act. Prime Minister Lee insisted that the law is necessary to maintain
Singapore’s racial harmony in the face of Islamic extremism in Southeast Asia.
A Strengthened Partnership with the United States. In July 2005,
President Bush and Prime Minister Lee signed the “Strategic Framework Agreement”
to formalize the growing bilateral security and defense relationship in
counterterrorism, counter-proliferation of weapons of mass destruction, joint military
exercises, policy dialogues, and shared defense technology. Bilateral military access
agreements allow the United States to operate resupply vessels from Singapore and
to use a naval base, a ship repair facility, and an airfield on the island-state.
Singaporean authorities have also shared information gathered from the detainees
with U.S. officials, providing detailed insights into JI and Al Qaeda’s structure,
methods, and recruiting strategies.
Bilateral and Multilateral Cooperation. Singapore has demonstrated its
commitment to fighting terrorism through a number of multilateral and bilateral
agreements. It was a founding member of the U.S.-led Proliferation Security
Initiative (PSI), a program that aims to interdict shipments of weapons of mass
destruction-related materials. It also was the first Asian country to join the Container
Security Initiative (CSI), a series of bilateral, reciprocal agreements that allow U.S.
Customs and Border Patrol officials at selected foreign ports to pre-screen
U.S.-bound containers. Singapore signed and ratified the U.N. Convention for the
Suppression of the Financing of Terrorism and has tightened its surveillance of
financial records. In 2005, Singapore reinforced or initiated existing cooperation
among terrorism-related agencies with neighboring and distant countries, including
Malaysia and Germany. In November 2005, the Singapore Armed Forces (SAF)
hosted counter-terrorism exercises, including hostage rescue and chemical and
biological attack response exercises, for special forces personnel from 19 Asian and
European countries.
Since 9/11, Singapore has increased intelligence cooperation with regional
countries and the United States. Singapore officials point to the arrest in Indonesia
of Mas Selamat Kastari, the alleged Jemaah Islamiyah Singapore cell leader and the
arrest in Thailand of Arifin Ali, a senior member of the same cell, as evidence of
successful intelligence sharing with counterparts in neighboring countries.
In addition to security countermeasures to prevent and respond to terrorist
attacks, Singapore has also addressed the ideological dimensions of Islamic

fundamentalism. The“Religious Rehabilitation Group” attempts to correct what it
dubs misrepresentations of the Islamic faith. To effectively address the ideological
aspects of religious extremism, Singaporean officials have urged Middle East
countries to pool resources with Asian partners. Turning to its ASEAN neighbors,
Singapore agreed to a pact with Indonesia, Malaysia, and Brunei ministers to oppose
violence and promote moderate Muslim values.
Emphasis on Maritime Security. Singapore is party to a United Nations-
administered international code–the International Ship and Port Facility Security
(ISPS) code to the Safety of Life at Sea (SOLAS) convention–that bolsters maritime
security; Singapore was one of the first ports to reach full compliance with the
required safety measures. Singapore has focused particular attention on maritime
security measures, urging other littoral states in Southeast Asia to work together to
protect critical shipping lanes. In 2004, Singapore launched joint naval exercises
with Australia and trilateral coordinated patrols of the Straits of Malacca with
Indonesia and Malaysia, in addition to introducing a joint tracking center on Batam
Island with Indonesia. In 2005, press reports indicated that the three states may
expand the protection of the Straits to include air protection as well. Many regional
security experts have noted that the demonstrated threat of piracy in the Straits is
increasingly being coupled with the threat of a major act of maritime terrorism.
Some terrorism specialists, however, have claimed that the chances of a radical
Islamic group launching a maritime attack have been overstated, and the money spent
to deter such an attack is disproportionate to the threat.
There were several key developments in Australia’s war against terror in 2005.
A second Bali bombing in October 2005 killed 23 including four Australians and
Australian police arrested 18 in an anti-terror operation in Sydney and Melbourne
that authorities claimed prevented an imminent and catastrophic attack against
Australia. The Howard Government also introduced anti-terror laws that have121
concerned civil libertarians and members of the Australian Muslim community. By
the end of 2005 Australia had also concluded 12 Memorandums of Understanding
on counter terrorism. Australia also pledged A$40.3 million over the next four years
to boost regional cooperation in the fight against terrorism.122
Australian involvement alongside the United States in the war against terror has
been staunch, as was highlighted by President Bush in his address to the Australian
Parliament on October 22nd, 2003. In his address, the President pointedly
acknowledged the valuable contribution made by Australia’s special forces in
Afghanistan and in Iraq. Prime Minister Howard was visiting Washington DC on
September 11, 2001, as part of the celebration of the 50-year anniversary of the
ANZUS alliance. Shortly after the attacks of that day, in which 22 Australian lives
were lost, Australia evoked the ANZUS Treaty to come to the aid of the United

121 “Terrorism Tops Australia’s 2005 News Bulletin,” Australian Associated Press,
December 27, 2006.
122 The Hon. Alexander Downer, Minister for Foreign Affairs, “Regional Counter-Terrorism
Package,” May 10, 2005.

States and subsequently committed Australian military forces to fight in Afghanistan
and Iraq. Australia’s commitment to the war on terror was redoubled as a result of
the Bali bombing, which killed 89 Australians, as well as by the September 9, 2004
attack on the Australian Embassy in Jakarta. Imam Samudra stated in his confession
of his role in the Bali bombing that Australians had been targeted in the Bali attack
for their ties to the United States and for their involvement in East Timor.123
Australia helped East Timor become an independent nation through its leading role
in 1999 in the International Force East Timor (INTERFET) and in the follow-on U.N.
Transitional Administration East Timor (UNTAET).
Whereas Southeast Asia has been described as the “second front” in the war on
terror by senior U.S. officials, it is Australia’s area of most immediate strategic
interest. Australia’s approach to its war on terror is outlined in a white paper
Transnational Terrorism: The Threat to Australia, prepared by the Department of
Foreign Affairs and Trade. JI’s mantiqi 4 was operating in Australia for years before
the Bali bombing of October 2002. There are approximately 340,000 Muslims in
Australia constituting approximately 4% of the population.124 Australia has been
working closely with Indonesian and other regional authorities to combat terrorism.
Australian Federal Police officers assisted Indonesia in finding suspects and tracking
the money trail used to finance the first Bali attack.125 Australian Federal Police also
assisted the investigation into the bombing of the Indonesian Peoples Representative
Council. In 2002, the two countries negotiated a MOU on Terrorism, in which they
pledged to cooperate on information and intelligence sharing, law enforcement,
money laundering and terrorist financing, cooperation on border control systems, and
aviation security.126 Australia has established an Ambassador for Counter Terrorism
and has concluded counter terror MOUs with several countries.
Australia is expanding its counter terrorism cooperation with Indonesia and
regional states while developing its own capabilities. Australia has helped finance the
Indonesian Center for Law Enforcement Cooperation in Jakarta.127 The center is to
support regional capacity building and also have an operational mandate to provide
support in response to specific terrorist threats or actual attacks.128 Australia held a
nationwide counter terror exercise in March 2004 that focused on preventing the use
of ships as weapons of mass destruction in an attack on Darwin. U.S.-owned
ConocoPhillips is currently developing a large liquid natural gas facility in Darwin.129
There are fears in Australia that Australia’s commitment to the U.S.-led war in Iraq

123 “JI Groups in Australia Watched,” The Daily Telegraph, February 11, 2003.
124 Richard Halloran, “The Rising East,” Honolulu Advertiser, November 14, 2004.
125 Daniel Clary, “Bali Trials List Might Widen,” The West Australian, May 15, 2003.
126 “Australia-Indonesia Joint Ministerial Statement,” Jakarta, Indonesia, March 11, 2003.
127 J. Frydenberg, “How to Step up the War on Terror in Our Backyard,” The Age, December

17, 2004.

128 The Hon. Alexander Downer, Minister for Foreign Affairs, “Indonesia Centre for Law
Enforcement Cooperation,” Department of Foreign Affairs and Trade, Australia, February

5, 2004.

129 “Tightened Security in Darwin,” Far Eastern Economic Review, April 1, 2004.

has made Australia more of a target for Islamic extremists. It was reported that the
CIA asked Hambali 200 questions on behalf of the Australian government. As a
result of this line of questioning it is reported that Hambali had planned on attacking
Australia but was unable to assemble an effective team to carry out the attack.130
It is now thought by leading analysts that JI was more active in Australia than
previously thought. Twenty individuals in Australia are thought to have received
terrorist training and another four await trial on terrorism charges.131 It has been
asserted that JI sent twin brothers Abdul Raham Ayub and Abdul Rahim, both of
whom had close connections with Al Qaeda, to Australia prior to the Bali bombing.
Rahim is thought to have been the JI leader in Australia. Another JI member in
Australia, Wandi, is thought to have had ties to Hambali and to have laundered funds
for JI. It is thought that Australia has been the source of much monetary support for
JI including one $1.5 million donation to the Philippines which was reportedly
detected by Philippines authorities. It is also thought that other funds went to JI in
Indonesia. An Australian convert to JI who reportedly met with Hambali, Jack
Roche, reportedly is serving a nine-year sentence in Australia after pleading guilty
to conspiring to bomb the Israeli embassy in Canberra.132 Former ASIO head Dennis
Richardson has also been quoted as saying that “...it is likely that Brigitte [a French
al-Qaeda suspect] and his associates would have carried out a terrorist attack in
Australia” had they not been thwarted by French-Australian co-operation.133
The reelection of both President Bush and Prime Minister Howard in 2004, who
have established a close relationship, will likely help facilitate coordination in the
two states’ fight against terrorism. Within this context, the United States will likely
continue to look to Australia to offer assistance particularly in Southeast Asia and the
Southwest Pacific. Australia’s contribution to regional security and counter terror
initiatives and focus on Indonesia will be of particular assistance.134 Australia has
reportedly committed to establishing six additional counter terror teams within the
Australian Federal Police that will have the capability to operate in the region.
Australia also held a meeting of regional special forces to discuss counter terror
measures.135 The United States released Australian Mamdouh Habib to Australia after
being held for three years in Guantanamo Bay for suspected terrorism. The Australian
Government believes Habib had ties to Al Qaeda.136 Australian David Hicks who is

130 “Hambali’s Plan to Attack Australia Misfired,” Jakarta Post, January 24, 2004.
131 Tom Allard, “Suspected Violent Extremists on Rise, ASIO Warns,” The Sydney Morning
Herald, November 6, 2004.
132 Mark Forbes, “Al-Qaeda, JI Links in Australia,” The Age, November 1, 2004. See also
Sally Neighbour, In the Shadow of Swords, (Sydney: Harper Collins, 2004).
133 Kate Gauntlett, “WE Bungled Terrorist Offer,” The West Australian, November 6, 2004.
134 Geoffrey Barker, “Howard and Bush Know the Appeal of Simple Nostrums,” Financial
Review, November 6, 2004.
135 J. Frydenberg, “How to Step up the War on Terror in Our Backyard,” The Age, December

17, 2004.

136 Cynthia Banham, Marian Wilkinson and G. Noonan, “Habib Comes Home to

thought to have fought for the Taliban and Al Qaeda has also been held in
Cambodia and Burma: New Countries of Convenience?
Two of the hallmarks of Al Qaeda and JI have been their mobility and
adaptability. The heightened scrutiny placed on JI operations in the major countries
in Southeast Asia has led to concerns that the terrorist network would establish or
step up operations in other countries that on the surface would appear to be unlikely
locales for Islamic terrorism to take root. Burma has a small Muslim minority (4%
of the total population of 43 million), many of whom have experienced
discrimination and severe restrictions on freedoms under the military junta (State
Peace and Development Council). Some groups, such as the Rohingya Muslims,
who have been persecuted by the current regime, could be receptive to recruitment
by extremist Islamic groups.138 During Indonesian authorities’ interrogation of Omar
al Faruq, the Al Qaeda leader reportedly admitted that JI had been attempting to forge
ties with radical Muslims in Burma.139 The Burmese government asserts that there
are terrorist elements among Burmese Muslims, linked to an al Qaeda network in
neighboring Bangladesh. However, the United States and many other governments
are unlikely to view these claims as credible because they have not been
independently verified and because the Burmese government may use such claims
as a pretext to attack the Muslim community as a whole.
Hambali, the Indonesian suspected of masterminding the 2002 bombing in Bali,
took refuge in Cambodia from September 2002 until March 2003, and reportedly
planned to use Cambodia as a base for launching further terrorist attacks.140 In
Cambodia in May and June 2003, four men — one Cambodian Muslim, two Thai
Muslims, and an Egyptian — were arrested in Phnom Penh for belonging to JI and
plotting to carry out terrorist attacks in Cambodia. The three non-Cambodians were
teachers at a Saudi-funded Islamic school that Cambodian authorities subsequently
shut down, expelling fifty foreign employees. The school was run by a charitable
foundation that is suspected of laundering money for JI and Al Qaeda. The
information leading to the arrests reportedly came from a tip provided by the United
States following the interrogation of a Singaporean JI operative who is said to have
met with and sent funds to the suspects in Cambodia.141 Since the withdrawal of

136 (...continued)
Surveillance and a Hostile PM,” Sydney Morning Herald, January 13, 2005.
137 P. Debelle, “Trial Ruling Raises Hopes as Hicks Moved,” Sydney Morning Herald,
November 10, 2004.
138 Andrew Selth, “Burma’s Muslims and the War on Terror,” Studies in Conflict and
Terrorism, Volume 27, No. 2 (March-April 2004).
139 Abuza, “Terrorism in Southeast Asia,” p. 15.
140 “Hambali Wanted Cambodia as Base for Attacks: Report,” Agence France-Presse.
141 Luke Hunt, “JI arrests Throw Spotlight on Cambodia’s Radical Muslims,” Agence
France Presse, May 28, 2003; Shawn Crispin, “Targets of a New Anti-Terror War,” Far

Vietnamese troops in the early 1990s, Cambodia’s Cham ethnic group, most of
whom are moderate Muslims, has seen a rise in Wahhabi influence and funding from
Wahhabi schools in the Middle East. The Cham make up less than 5% of
Cambodia’s 12.5 million population, which is predominantly Buddhist. In May
2005, a group identifying itself as “Allah” reportedly threatened to attack the
embassies in Phnom Penh of Australia, Canada, the United States, and other
countries cooperating with the U.S.-led war in Iraq.142
Options and Implications for U.S. Policy
Strategies for Combating Terrorism in Southeast Asia
The 9/11 Commission recommends conceptualizing the battle against Islamist
terrorism as a two-pronged campaign on the one hand aimed at disrupting the
leadership of Al Qaeda, Jemaah Islamiyah, and like-minded terrorist networks and
on the other hand competing against the rise of radical ideologies within the Islamic
world that inspire terrorism.143 To date, U.S. policy in Southeast Asia has
emphasized the first goal, which is more immediate and requires an emphasis on the
policy tools necessary to kill and capture specific individuals, locate and destroy
terrorist training facilities, and identify terrorist financing networks.
The second goal is perhaps less urgent in the immediate term, but more
important in the longer term. It also is more complex, for essentially it aims at
reducing the appeal of violent Islamism by strengthening national governments’
ability to provide their Muslim citizens with an attractive alternative. Although
Southeast Asian societies and governments in general are more tolerant,
representative, and responsive than those in the Middle East and South Asia, Islamist
terrorist groups have been able to exploit the sense of alienation produced in part by
the corruption and breakdown of institutional authority in Indonesia and by the
marginalization of minority Muslim groups in the southern Philippines and southern
Additionally, to date the U.S. approach to fighting terrorism in Southeast Asia
primarily has been bilateral — rather than multilateral — in nature, and generally has
been limited to the law enforcement — rather than the military — realm. In the near
term, barring another major terrorist attack, it is difficult to foresee these features of
U.S. strategy changing since they are based upon features of international relations
in Southeast Asia: relatively weak multilateral institutions, the poor history of
multilateral cooperation, and the wariness on the part of most regional governments
of being perceived as working too closely with the United States. Addressing these
deficiencies could be elements of the long-term goal of competing against terrorist

141 (...continued)
Eastern Economic Review, July 10, 2003; Abuza, “Terrorism in Southeast Asia,” p. 16.
142 “Threat to Missions in Cambodia,” CNN.com.
143 The 9/11 Commission Report, p. 361-365.

Decapitation. Thus far, the strategy of arresting Jemaah Islamiyah’s
leadership is thought to have crippled JI’s capabilities significantly. If the
International Crisis Group’s observation of factions within JI is correct, it may mean
that a continued push to arrest the network’s leadership could dramatically reduce
JI’s ability to threaten Western targets directly. The arrests likely would
disproportionately target JI’s more radical leaders, perhaps giving more prominence
to the “bureaucrats” who have a longer time horizon and reportedly believe that
violence against Westerners undermines the ultimate objective of establishing sharia
in the region. Additionally, it appears that middle and lower-level JI functionaries’
level of commitment may not be as fanatical as commonly thought. Some plotters
reportedly have had second thoughts about participating in particular operations,
indicating that close intelligence sharing could help governments identify members144
who could be induced to desert.
Military Options. Yet, the apparent ability of JI to remain potent despite the
elimination of most of its leadership indicates that a decapitation strategy alone is
insufficient. There are reports that some U.S. military officials have expressed a
desire to conduct surveillance and/or act upon surgical strike plans, including covert
actions, targeting terrorist training camps in Southeast Asia.145 Attacking camps
operated by JI and/or the MILF in Mindanao may be particularly attractive, as
Mindanao may be performing a crucial role as a regrouping and training area for JI
However, policy makers would face the question of balancing any gains from
eliminating JI camps with the likely longer-term risks. The two countries with
suspected JI camps, Indonesia and the Philippines, are particularly sensitive to the
presence of U.S. troops operating in their territory, as evidenced by Jakarta’s
reluctance to allow U.S. pilots to conduct aerial training exercises in Indonesian
airspace while U.S. aircraft carriers perform relief and reconstruction work in Aceh
following the December 2004 tsunami. Thus, if covert military actions were carried
out by U.S. soldiers and were discovered, the revelations would likely inflame anti-
American opinion, regardless of whether they were sanctioned by the host
government. The likely backlash would then make it much more difficult for
Southeast Asian national and local leaders to support these and other U.S. anti-
terrorism actions. Furthermore, even if camps are successfully eliminated, it is likely
that they could be rebuilt and/or relocated in relatively short order.
In weighing military options, U.S. policymakers would face the question of
balancing the advantages and disadvantages of conducting the operations with U.S.
troops or rely on local forces, of carrying out operations overtly or covertly, and of

144 Rohan Guanaratna, “Al-Qaeda’s Operational Ties with Allied Groups,” Jane’s
Intelligence Review, February 1, 2003.
145 Barton Gellman, Washington Post, “Secret Unit Expands Rumsfeld’s Domain,” January
23, 2005. Additionally, in the days after the September 11 attacks, at least one senior
Pentagon official floated the idea of taking military action against terrorist targets in
Southeast Asia as a “surprise” alternative to attacking Afghanistan. The 9/11 Commission
Report, p. 559, note 75; Douglas Feith, “A War Plan That Cast A Wide Net,” Washington
Post, August 7, 2004.

notifying the local government of such actions beforehand or conducting them
without prior notification. Actions taken without local approval could well be
regarded by many in the region as an act of war.
Short- and Long-Term Capacity-Building Strategies. Other
counterterrorism strategies include placing a greater emphasis on attacking the
institutions that support terrorism, and building up regional governments’
institutional capacities for combating terrorist groups and for reducing the sense of146
alienation among Muslim citizens. Options include:
!Placing priority on discovering and destroying terrorist training
centers, which have proven extremely important to JI and the MILF,147
in particular;
!Increasing the U.S. Pacific Command’s use of international
conferences and exercises aimed at combating terrorism and piracy,
such as through PACOM’s proposed regional maritime security
!Strengthening the capacities of local government’s judicial systems,
through training and perhaps funding, in an effort to reduce the
corruption and politicization of the judicial process;
!Working with Indonesia, the Philippines, and other countries to
better manage communal tensions and identify religious flash points
before they erupt. Sectarian violence has proven to be fertile ground149
for JI and other terrorist groups to recruit and raise funds;
!Building up state-run schools, so that Muslims are less likely to send
their children to radical madrassas where extremist brands of Islam
are propagated. The 9/11 Commission recommends creating a new
multilateral “International Youth Opportunity Fund” that would seek
to improve primary and secondary education in Muslim
communities.150 The Bush Administration moved in this direction
in October 2003, when it launched a $157 million program to help
improve the quality of Indonesian schools. The initiative has been
criticized on the grounds that unlike in Pakistan and the Middle East,
where madrassas often are the best opportunity for an education, in
Southeast Asia, many JI members hail from the middle class, and

146 Abuza, “Funding Terrorism in Southeast Asia,” p. 10-11.
147 Jones, “Indonesia Backgrounder,” p. ii.
148 United States Pacific Command Joint Interagency Coordination Group for Combating
Terrorism, “Strategy for Regional Maritime Security Initiative,” Version 1.0, November,


149 Sidney Jones, “Terrorism In Southeast Asia, More Than Just JI,” Asian Wall Street
Journal, July 29, 2004.
150 The 9/11 Commission Report, p. 378.

most recruitment appears to occur in mosques or on university
cam puses; 151
!Expanding educational exchanges, similar to the Fulbright program,
so that future elites have thorough exposure to the United States;
!Strengthening civil society and the democratic process;
!Pursuing policies, such as negotiating free trade agreements and
promoting the multilateral Doha Development Agenda trade talks,
that encourage economic development;152
!Increasing regional cooperation on a multilateral and bilateral basis
with key governmental institutions involved with the war against
!Providing assistance and training to developing regional counter
terrorism centers;
!Assisting in developing frameworks such as harmonized extradition
agreements and evidentiary standards to more effectively prosecute
terrorists and facilitate investigations and data sharing with regional
!Building up the capabilities of countries’ coast guards and navies to
better combat piracy, gun running, and other types of smuggling,
particularly in the Straits of Malacca and the waters between
Sulawesi and the southern Philippines.153 USPACOM’s proposed
regional maritime security initiative envisages this type of
cooperation. The U.S. military could play a role here, perhaps in
coordinating with Japan, the Coast Guard of which has been
conducting bilateral exercises with selected Southeast Asian
countries. Two difficulties are that Malaysia only recently
established a Coast Guard, and Indonesia has nearly a dozen
agencies that claim responsibility for guarding Indonesian waters, in
which about one-quarter of the world’s piracy incidents occurred in


!The 9/11 Commission argues that tracking terrorism financing “must
remain front and center in U.S. counterterrorism efforts.”
Notwithstanding increased police cooperation, most Southeast Asian
countries do not appear to have made commensurate efforts to

151 Jones, “Terrorism In Southeast Asia, More Than Just JI.”
152 The 9/11 Commission Report, p. 378-79; Robert Zoellick, “Countering Terror With
Trade,” The Washington Post, September 20, 2001.
153 The Stanley Foundation, “US Security Relations With Southeast Asia: A Dual
Challenge. Southeast Asia in the Twenty-First Century: Issues and Options for US Policy,”
Policy Bulletin, March 2004, p.1-2.

locate, freeze, and at a minimum disrupt the flow of the assets of
Islamic terrorist groups. Although shutting down informal financing
mechanisms such as cash donations and the informal hawala system
of transferring money would be next to impossible, feasible actions
include shutting down charities linked to terrorist groups, monitoring
front companies and legitimate businesses linked to terrorist groups,
and establishing a regional clearing house for intelligence sharing.154
Concurrently, monitoring of terrorist money can be used as an
important intelligence tool to better understand how terrorist
networks operate.155
!As part of ongoing bilateral cooperation, U.S. officials could
emphasize increased regulation, transparency, and enforcement in
individual countries’ financial sectors.
Public Diplomacy. Ultimately, convincing regional governments to increase
anti-terrorism cooperation will likely depend upon reducing the political costs of
doing so. Muslim Southeast Asia currently is undergoing something of a spiritual
awakening, with Islamic consciousness rising and influencing the opinion of
moderate Muslims. Polls indicate that U.S. actions in the Middle East, particularly
in Israel and Iraq, have led to a steep rise in anti-Americanism making overt
cooperation with U.S. counterterrorism operations more difficult, as increasing
numbers of Muslims in Southeast Asia see U.S. policy as anti-Muslim. Singapore’s
former Prime Minister Goh Chok Tong, for instance, has argued that “a more
balanced and nuanced approach [by the United States] towards the Israeli-Palestinian
conflict ... must become a central pillar to the war on terrorism” in order to maintain
credibility in Southeast Asia.156
Additionally, there appears to be a perception among some Southeast Asians
that the United States has relied too heavily on “hard” (military) power to combat
terrorism, not only in Afghanistan and Iraq, but also in Southeast Asia. Malaysian
Defense Minister Najib Razak, for instance, has stated that “terrorism cannot be
bombed into submission ... the underlying legitimate grievances that allow for such
extremists to gain support” must be addressed. He advocates “a judicious mix of
hard and soft force” to prevail against terrorism. Some regional academics also have
concluded that America’s “highly militarized approach” to the war against terror in
Southeast Asia may be inadequate to neutralize the threat and may “even backfire.”
“The embers of radical Islamist terrorism can only be doused by the adoption of a
comprehensive approach that addresses a host of real or perceived social, economic,157
political, and ultimately ideological challenges.” Secretary of Defense Rumsfeld

154 Abuza, “Funding Terrorism in Southeast Asia,” p. 56-68.
155 The 9/11 Commission Report, p. 382.
156 Muray Hiebert and Barry Wain, “Same Planet, Different World,” Far Eastern Economic
Review, June 17, 2004.
157 See Seng Tan and Kumar Ramakrishna, “Interstate and Intrastate Dynamics in Southeast

reportedly cautioned regional leaders against making a “separate peace” with
terrorists and equated such action with the appeasement of Adolf Hitler.158 While
these perceptions of an overly militaristic U.S. response in Southeast Asia may be
overblown — particularly by being colored by U.S. politics in the Middle East —
they may indicate a disconnect between the United States approach to the war on
terror and its regional friends and allies. Such a division has the potential to limit the
degree to which regional states will cooperate with the United States in the war on
To counter these sentiments, the United States could expand its public
diplomacy programs in Southeast Asia to better provide an explanation for U.S.
actions in the region and other parts of the world. Many of these programs were
reduced significantly in the 1990s, after the end of the Cold War. The 9/11
Commission specifically recommends increasing funding to the Broadcasting Board
of Governors, the independent but government-financed agency that is responsible
for all U.S. government and government sponsored, non-military, international
broadcasting, including the Voice of America (VOA).159 Applied to Southeast Asia,
such a step could include expanding VOA’s existing Indonesian language broadcasts
and adding broadcasts in Javanese and other Indonesian dialects, as well as in Malay
and Tagalog.
Multilateral Efforts. Finally, the ease with which Al Qaeda, JI and other
groups have transferred personnel, money, weapons, and information across borders
indicates that thwarting terrorist activities will likely require a coordinated,
international response in a region where multinational institutions — including
ASEAN — and cooperation are weak. Greater border controls in particular can help
disrupt terrorists’ travel activities. The importance of multinational intelligence-
sharing and extradition agreements is underscored by reports that many captured Al
Qaeda and JI members have provided authorities with useful information that has led
to further arrests and the discovery of new plots.
A number of Southeast Asian states have increased anti-terrorist cooperation,
both with the United States and with each other. In particular, there appears to be a
dramatic improvement in the level of intelligence sharing among national police
forces. Cooperation among Singapore, Malaysia, the Philippines, and the United
States appears to have been particularly effective, leading to the arrests of dozens of
suspected JI members, including several top leaders. Another sign of increased
attention given to terrorism occurred in July 2003, when the Southeast Asia Regional
Center for Counter-Terrorism opened in Kuala Lumpur. The center houses
researchers and hosts training sessions for regional officials. In August 2002, the
United States and all ten members of ASEAN signed an agreement to cooperate in
counterterrorism activities. The agreement calls for signatories to freeze terrorist

157 (...continued)
Asia’s War on Terror,” SAIS Review, Spring, 2004.
158 Murray Hiebert and Barry Wain, “Same Planet, Different World,” Far Eastern Economic
Review, June 17, 2004.
159 The 9/11 Commission Report, p. 375-77.

groups’ assets, improve intelligence sharing, and improve border controls.160
Delegates attended the second ASEAN Regional Forum Inter-sessional meeting on
Counterterrorism and Transnational Crime in March 2004 where they discussed
transport systems as potential terrorist weapons. The meeting was co-chaired by the
Philippines and Russia.161 The ASEAN Regional Forum has begun to study some
elements of USPACOM’s proposed regional maritime security initiative, particularly
strengthening transport security, and conducting joint navy and coast guard
simulations and exercises.162
United States-Indonesian anti-terrorism cooperation improved significantly after
the Bali bombing. Fears that the United States’ war against Iraq would inflame the
country were proven to be largely unjustified, though U.S. policy toward Iraq and
Israel are the two key issues contributing to the declining popularity of the United
States in Indonesia. Though more recent bombings have demonstrated that terrorists
are still operating in Indonesia, Indonesian police efforts, including widespread
arrests of suspected JI members, have set back the radical Islamic agenda in
Indonesia and helped moderate Islamic groups improve their position. One of the key
reasons for Indonesia’s more aggressive stance against JI is the growing post-Bali
perception that the network is a threat not just to Western interests in Indonesia but
to the Indonesian government and society as well.
The potential for a nationalist backlash against working too closely with the
United States continues to exist, perhaps raising the need for a heavy reliance upon
relatively unobtrusive forms of counter terrorism cooperation. Counter terror
cooperation options include intelligence sharing, cooperation in police investigations,
training in border and immigration controls, and other cooperative activities. The TNI
generally has more effective domestic intelligence capabilities than the national
police, which until January 2001 were part of the military establishment. The Bush
Administration has moved forward with its desire to reestablish military-to-military
ties with Indonesia. The central role that the military plays in Indonesia highlights
the importance of any relationship with the military. To this end the United States
has established a counter terrorism fellowship program with Indonesia. On the other
hand, the TNI is widely viewed as among the most egregious actors in Indonesian
rights abuses.
One policy issue that Congress may wish to consider is how best to support
moderate Islamic elements in Indonesia in what is developing into a struggle with
more conservative, and in some cases extremist, forms of Islam in Indonesia. It
would not be in the United States’ interests if a more radical form of Islam came to
dominate Indonesia. In such a situation, extremist groups would have more ability

160 United States of America-ASEAN Joint Declaration for Cooperation to Combat
International Terrorism, August 1, 2002.
161 “Terrorism on Wheels, On Wings,” Manila Standard, March 31, 2004.
162 BBC Monitoring Asia Pacific, “ASEAN Forum Members Affirm Need to Boost
Transport Security Against Terrorism,” July 2, 2004.

to operate and would likely have a larger pool of disaffected Indonesians from which
to draw their recruits. Some observers suggest that the United States should step up
its assistance to democratization in Indonesia. From this perspective, the sooner
Indonesia establishes political stability and develops deeper democratic institutions,
the sooner it will be able not only to increase cooperation against terrorism but also
rein in the Indonesian military and gain greater accountability from it.
The Philippines
The delicate internal political situations in the Southeast Asian countries
affected by Islamic radicalism and terrorism impose serious limitations on U.S.
freedom of action. This currently is highlighted by the difficulties in Philippine-U.S.
negotiations over developing a second U.S. program of military support for Filipino
military operations against Abu Sayyaf. U.S. interests have been threatened by MILF
training of JI personnel and the flow of terrorists and terrorist weapons between
Mindanao and the Indonesia island of Sulawezi.
During the Balikatan operation of 2002, the Bush Administration and the
Philippine government sought to avoid a U.S. confrontation with the MILF.
However, mounting evidence of MILF support for JI reportedly led the Bush
Administration in late 2002 to consider placing the MILF on the U.S. official list of
foreign terrorist organizations. President Arroyo reportedly convinced U.S. officials
not to take that action in the interest of preserving the cease-fire with the MILF. If
Manila’s truce with the MILF collapses, the Philippine Army — elements of which
favor restarting military actions against the MILF — undoubtedly would use recently
supplied U.S. military equipment against these groups. The Philippine government
might change policy and encourage U.S. action against the MILF at least in a role
similar to that in the Balikatan exercise against Abu Sayyaf. In order to avoid this,
the Bush Administration has supported President Arroyo’s attempts to restore the
cease-fire that was on the verge of collapse in March-April 2003. However,
Philippine cease-fires with the MILF have not yet addressed the major U.S. interest
of ending MILF support and assistance to JI. A key issue for the immediate future
is whether the international observer group slated to monitor the current cease-fire
will be installed and whether it, coupled with Malaysia role, will dampen MILF
cooperation with JI. Reports in early 2005 indicated that MILF-JI training may have
President Arroyo’s narrow election victory in May 2004 seemed to augur well
for Philippine-U.S. counterterror cooperation. However, relations have been strained
by her decision to hasten the withdrawal of the small Filipino military contingent in
Iraq to secure the release of a Filipino held hostage by Iraqi insurgents. U.S. officials
criticized her decision. The Pentagon has indicated that the United States will
continue to supply weapons to the AFP, but U.S. officials have indicated that other
components of the security relationship could be affected by Arroyo’s decision.163

163 Illustre, Jennie L. “U.S. signals no pause in military aid.” Philippine News (San
Francisco), August 4, 2004.

Counterterrorism cooperation with Thailand faces fewer political constraints
than do efforts with most other Southeast Asian states. Security cooperation with
Thailand is well established: ties were institutionalized in 1962 with the U.S.-Thai
military pact, after which Thailand provided bases to support U.S. operations in
Vietnam. The relationship continued through the Cold War, and today includes
annual joint military exercises and extensive intelligence coordination. However, the
Thai authorities remain sensitive to perceptions that they are too closely aligned with
the United States. According to press reports, Thai officials requested that the Bush
Administration refrain from publicizing Thailand’s support of the invasion of Iraq.164
After remaining neutral during the combat phase, Thailand sent a contingent of over
450 troops to Karbala to join the multinational force under Polish command. The
scheduled pull-out was completed in September 2004. Other Thai officials have
voiced concern that Thailand’s involvement in Iraq could fuel Islamic militancy on
its own soil.165
Although the recent violence in the southern provinces may prove otherwise,
Thailand has been considered attractive to terrorists not as a base of operations, but
as a meeting place or transit point because of its unrestrictive, tourist-friendly border
controls. Maintaining a low profile on bilateral security cooperation, particularly in
the intelligence realm, may prove helpful in luring terror network operatives to the
country, where Thai and American intelligence could monitor their activities.
Downplaying U.S. support might be prudent in the Muslim region, where local
groups have demonstrated a strong distrust of American — as well as central Thai
government — motives.
Role of Congress/Legislation
Appendix A contains tables detailing U.S. assistance to Indonesia, the
Philippines, and Thailand since the September 11, 2001 attacks.
Administration officials and some Members of Congress have struggled to find
a way to reconcile the need to gain the cooperation of the Indonesian military (TNI)
with the desire to keep pressure on the military to accept civilian control and accept
accountability for past human rights violations. These include the brutal repression
against peaceful pro-independence supporters in East Timor in 1999, which became
the independent nation of Timor Leste on May 20, 2002, under United Nations
supervision. Some members of Congress have also been concerned about the lack
of progress towards identifying and bringing to justice the perpetrators of the attacks
on American teachers and students from an international school near Timika, in West

164 Raymond Bonner, “Thailand Tiptoes in Step with American Antiterror Effort,” New York
Times. June 7, 2003.
165 “Thai PM Says Troops Will Pull Out of Iraq if Unable to Work,” Agence France Presse.
April 20, 2004.

Papua Province, that is connected to U.S.-based Freeport-McMoRan Copper and
Gold Inc.
The “Leahy” Amendment Restriction on Military Aid. For more than
a decade, Congress has restricted the provision of military assistance to Indonesia due
to concern about serious human rights violations by the Indonesian military (TNI).
Congress first took the initiative by enacting legislation prohibiting International
Military Education and Training (IMET) and arms sales to Indonesia in October
1992, under the so-called “Leahy Amendment” to the FY1992 foreign operations
appropriation bill. In subsequent years, Congress regularly included similar or related
human rights conditions to successive annual foreign operations appropriations bills.
The specific conditions have varied over time, but few of them have been fulfilled
to date. Some in Congress have been particularly dissatisfied with the lack of
accountability of TNI commanders for the atrocities in East Timor in 1999. Trials
of 15 commanders and one police official in 2003 resulted in 12 acquittals and four
convictions that were overturned on appeal.
Partly in response to congressional pressure, President Clinton in September
1999 suspended all military, economic, and financial aid to Indonesia. The aid cutoff
was imposed in response to a wave of mass killings and destruction of property
perpetrated by the Indonesian army and locally-recruited paramilitary in revenge for
an overwhelming vote for independence by East Timorese in an August 30, 1999166
U.N.-supervised plebiscite. However, in 2000, the Clinton Administration lifted
part of the ban to allow the sale of U.S. spare parts for Indonesian C-130 military
transport aircraft. In January 2005, as part of U.S. assistance to Indonesia in the
aftermath of the tsunami disaster, Secretary of State Colin Powell announced the sale
of C-130 spare parts would go forward.
Appendix B contains a legislative history of the Leahy Amendment and its
variations since FY2002.
The Impact of 9/11. Following the September 11, 2001 terrorist attacks,
Congress and the Bush Administration engaged in extensive informal negotiations
about ways to support increased anti-terrorist cooperation with Indonesia while
continuing to press the Indonesian government about other U.S. concerns. A main
policy consideration has been the argument that the TNI generally has more effective
domestic intelligence capabilities than the national police, which until January 2001
were part of the military establishment. For FY2002-FY2003, Congress provided
funds to allow the Department of Defense to provide counterintelligence training and
also allowed the provision of funds for Expanded International Military Education
and Training (E-IMET), which is designed to provide training in human rights and
respect for democracy.
The U.S. military’s participation in tsunami disaster relief in Aceh in January-
February 2005 resulted in cooperative relief measures with the TNI, including sales
of the C-130 spare parts. The Bush Administration saw this and the subsequent

166 Jim Lobe, “U.S. Suspends Military Ties with Indonesia.” Asia Times, Sept. 11, 1999

peace agreement between Indonesia and Acehnese insurgents as an opportunity to
restore full military to military ties with the TNI. In February 2005, the Secretary of
State issued a certification, required by the FY 2005 Leahy amendment, that
Indonesia was cooperating with the FBI’s investigation into the attack on the
Americans in Papua and therefore had satisfied the congressional conditions for the
resumption of full Indonesian participation in the IMET program. In May 2005, the
Administration resumed Foreign Military Sales (FMS) of non-lethal U.S. articles to
Indonesia and lobbied hard in Congress for resuming FMS of lethal defense articles.
The Administration secured this in the FY 2006 foreign operations appropriations
bill, P.L. 109-102. While the Leahy amendment in this bill continued to set out the
conditions in past bills for sales of lethal defense equipment, it added a clause giving
the Secretary of State authority to waive the conditions on grounds that a waiver was
“in the national security interests of the United States.” In November 2005, the
Secretary of State issued the waiver.

Other CRS Products Dealing with Terrorism in Asia
CRS Report RL32259. Terrorism in South Asia.
CRS Report RL32394. Indonesia: Domestic Politics, Strategic Dynamics, and
American Interests.
CRS Report RS20572. Indonesian Separatist Movement in Aceh.
CRS Report RL33233. The Republic of the Philippines: Background and U.S.
CRS Report RS20697. Philippine-U.S. Security Relations.
CRS Report RL31265. Abu Sayyaf: Target of Philippine-U.S. Anti-Terrorism
CRS Report RL32129. Malaysia: Political Transitions and Implications for U.S.
CRS Report RS20490. Singapore: Background and U.S. Relations.
CRS Report RS21358. Australia: Background and U.S. Relations.
CRS Report RS21903. Islam in South and Southeast Asia.
CRS Report RL32223. Foreign Terrorist Organizations.
CRS Report RL31119. Terrorism: Near Eastern Groups and State Sponsors, 2002.
CRS Report RS21529. Al Qaeda after the Iraq Conflict.
CRS Report RL32120. The “FTO List” and Congress: Sanctioning Designated
Foreign Terrorist Organizations.
CRS Report RL32058. Terrorists and Suicide Attacks.
CRS Report RL31831. Terrorist Motivations for Chemical and Biological Weapons
Use: Placing the Threat in Context.
CRS Report RL31152. Foreign Support of the U.S. War on Terrorism.
CRS Report RL31811. Appropriations for FY2004: Foreign Operations, Export
Financing, and Related Programs

Appendix A: U.S. Assistance to Indonesia, the
Philippines, and Thailand Since September 2001
Table 1. U.S. Assistance to Indonesia, FY2002-FY2006
($ in Millions)
TotalFYFY 2006
ProgramFY 2002FY 2003FY 2004 FY02- 2005(Est.)
Economic and Development Assistance
Child Survival/Health (CSH)35.5731.9634.00101.5237.1028.02
Development Assistance (DA)38.70 39.0231.29109.0127.8433.21
Economic Support Funds (ESF)50.0059.6149.71159.3268.4869.30
PL. 480, Title II Food Aid5.6729.546.6041.8111.9018.19
Total Economic Assistance129.94160.12121.60411.66145.32148.72
Security Assistance**
International Narcotics4.00--4.00-4.95
Control& Law Enforcement
International Mil. Education &0.410.28.591.150.730.79
Training (IMET)*
Foreign Mil. Financing (FMF)-- -0.00-1.00
Nonproliferation, Anti-
Terrorism, Demining & Related
Total Security Assistance**12.411.296.5719.916.0312.49
Total Economic and Security 142.35161.41 128.17431.58151.985161.21
Source: Department of State, FY 2006 International Affairs Budget Request; Foreign Operations,
Export Financing, and Related Programs Appropriations Act, 2006 (P.L. 109-102).
*Civilians only FY2002-04
** The military assistance figures do not include counterterrorism funds from the FY2002 anti-
terrorism supplemental appropriations (P.L.107-206), which provided up to $4 million for law
enforcement training for Indonesian police forces and up to $12 million — of which the Bush
Administration allocated $8 million — for training and equipping Indonesian police to respond
to international terrorism.

Table 2. U.S. Assistance to the Philippines, FY2002-FY2006
($ in Millions)
TotalFY FY2006
ProgramFY 2002FY 2003FY 2004 FY02-2005 (Est.)
Economic and Development Assistance
Child Survival/Health (CSH)25.6022.9229.3577.8727.0522.67
Development Assistance (DA)24.4628.2122.0774.7327.5825.52
Economic Support Funds (ESF)21.0045.0017.6583.6530.7019.80
Peace Corps2.172.622.777.562.842.97
Total Economic Assistance73.2298.7571.83243.8188.1770.96
Security Assistance
International Narcotics Control&-- 2.00
Law Enforcement (INCLE)
International Mil. Education &2.032.402.707.133.002.90
Training (IMET)
Foreign Mil. Financing (FMF)19.0049.8719.8888.7529.7629.70
Foreign Mil. Financing (FMF) -25.00--25.00--
Nonproliferation, Anti-Terrorism,0.102.09-2.190.60 5.15
Demining & Related (NADR)
Total Security Assistance46.0352.2724.58122.8836.7339.75
Total Economic and Security119.25151.02 96.41366.69124.90110.71
Source: Department of State, FY 2006 International Affairs Budget Request; Foreign
Operations,Export Financing, and Related Programs Appropriations Act, 2006 (P.L. 109-102).
Table 3. U.S. Assistance to Thailand, FY2002-FY2006
($ in Millions)
TotalFYFY 2006
ProgramFY 2002FY 2003FY 2004 FY02- 2005 (Est.)
Economic and Development Assistance
Child Survival/Health (CSH) 1.001.50- 2.50- -
Development Assistance (DA) 0.75 1.25 -2.00--
Economic Support Funds (ESF)- - -0.000.921.00
Peace Corps1.271.821.844.932.242.37
PL. 480, Title II Food Aid---0.00--
Total Economic Assistance 3.024.57 1.849.433.163.37
Security Assistance
International Narcotics Control&4.003.702.009.701.611.00
Law Enforcement (INCLE)
International Mil. Education &1.751.772.455.972.522.40
Training (IMET)
Foreign Mil. Financing (FMF) 1.301.991.004.291.491.48
Nonproliferation, Anti-Terrorism,0.720.200.381.300.751.00
Demining & Related (NADR)
Total Security Assistance7.77 7.66 5.8321.256.375.88
Total Economic and Security10.7912.237.6730.689.539.25
Source: Department of State, FY 2006 International Affairs Budget Request; Foreign Operations,
Export Financing, and Related Programs Appropriations Act, 2006 (P.L. 109-102).

Appendix B: Restrictions on Aid to Indonesia Since
the “Leahy Amendment” to the FY1992 Foreign
Operations Appropriations Act
For more than a decade, Congress has restricted the provision of military
assistance to Indonesia due to concern about serious human rights violations by the
Indonesian military (TNI), most notably the massacre of hundreds of people
participating in a pro-independence rally in Dili, East Timor, in November 1991.
Congress first took the initiative by enacting legislation prohibiting International
Military Education and Training (IMET) and arms sales to Indonesia in October
1992, under the so-called “Leahy Amendment” to the FY1992 foreign operations
appropriation bill. Section 599H of H.R. 5368, sponsored by Senator Patrick Leahy,
of Vermont, provided that none of the funds appropriated for International Military
Education and Training (IMET) could be made available to Indonesia unless by
December 15, 1992, the Secretary of State provided the Committees on
Appropriations with a certification verifying the fulfillment by the Indonesian
government of three conditions:
(1) special emphasis is being placed on education of Indonesian military
personnel that will foster greater awareness of and respect for human rights and
that will improve military justice systems;
(2) special emphasis is also being placed on education of civilian and military
personnel that will foster greater understanding of the principle of civilian
control of the military; and
(3) the Secretary of State will use all available and appropriate means to ensure
there is progress on the East Timor situation, such as the full availability of legal
remedies under Indonesian law to all civilians convicted in connection with the
November 1991 East Timor incident, increased access for human rights groups
to East Timor, and constructive cooperation with the United Nations Secretary
General’s efforts to promote dialogue between Indonesia and Portugal to resolve
issues concerning East Timor.” (Sec. 599H, P.L. 102-391)
In subsequent years, Congress regularly included similar or related human rights
conditions to successive annual foreign operations appropriations bills. The Clinton
Administration either acquiesced or did not object strongly to congressional
prohibitions and conditionality on military assistance to Indonesia, despite its general
opposition to legislative restraints on the President’s authority to conduct foreign
policy. Partly in response to congressional pressure, President Clinton in September
1999 suspended all military, economic, and financial aid to Indonesia. The aid cutoff
was imposed in response to a wave of mass killings and destruction of property
perpetrated by Indonesian army backed militias in revenge for an overwhelming vote
for independence by East Timorese in an August 30, 1999, U.N.-supervised

167 Jim Lobe, “U.S. Suspends Military Ties with Indonesia.” Asia Times, Sept. 11, 1999

In action on the FY2001 Foreign Operations Appropriations (P.L. 106-
429/H.R. 5526), following the 9/11 attacks, Congress made Indonesia eligible for
International Military Education and Training (IMET) for the first time in several
years, but only in the “expanded” version, known as E-IMET which emphasizes
respect for human rights and civilian control of the military. However, Sec. 579 of
the same legislation banned both IMET and Foreign Military Sales Financing (FMF)
for Indonesia unless the President determined and reported to Congress that the
Indonesian government and armed forces were fulfilling six requirements relating to
East Timor. These included facilitating the return of East Timorese refugees from
West Timor and bringing to justice “members of the military and militia groups
responsible for human rights violations in Indonesia and East Timor.”
FY2002 Foreign Operations Appropriations — Seven Criteria for
IMET and FMF. Section 572 (a) of P.L. 107-115 (H.R. 2506) allowed Indonesia’s
participation in the Expanded IMET program without conditions, but made FMF
available only if the President determined and reported to Congress that the
Indonesian government and Armed Forces were effectively addressing seven human
rights issues. These were similar to the those in the FY2001 legislation, but they also
required certification that Indonesia was allowing “United Nations and other
international humanitarian organizations and representatives of recognized human
rights organizations access to West Timor, Aceh, West Papua, and Maluka,” and
“releasing political detainees.”
FY2002 Supplemental Appropriation for Combating Terrorism (P.L.
107-206/H.R. 4775). In an effort to promote anti-terrorism cooperation without
abandoning U.S. human rights concerns, Congress focused U.S. assistance on the
Indonesian national police, a body that had been separated from the Indonesian
military in 1999 as part of an effort by the post-Suharto reformist government to
reduce the role of the TNI. The FY2002 anti-terrorism supplemental appropriations
provided up to $4 million for law enforcement training for Indonesian police forces
and up to $12 million — of which the Bush Administration allocated $8 million —
for training and equipping Indonesian police to respond to international terrorism,
including the establishment of a special police counterterrorism unit.
FY2003 Foreign Operations Appropriations (P.L. 108-7/H.J.Res. 2).
The 107th Congress did not complete action on the FY2003 foreign operations
appropriations bill (S. 2779), which carried over to the 108th Congress. Signed into
law on February 20, 2003, the FY2003 measure included a shorter revised list of
conditions on foreign military sales financing funding than was included in the
FY2002 appropriation. Military education and training assistance continued to be
restricted to E-IMET. The bill also earmarked $150 million in economic support
funds for Indonesia, of which not less than $10 million is to be used for programs and
activities in the troubled state of Aceh and not less than $5 million for reconstruction
in Bali. In addition, the FY2002 appropriation also provided not less than $25
million for the Democratic Republic of Timor-Leste (East Timor).
Sec. 568 of the FY2003 appropriations bill included a substantially shorter list
of certification requirements than previous years. It banned foreign military sales
financing funding for lethal items to the Indonesian military unless the President
certified to Congress that

(1) the defense ministry is suspending members of the military who “have been
credibly alleged to have committed gross violations of human rights, or to have
aided or abetted militia groups”;
(2) the government of Indonesia is prosecuting such offenders and the military
is cooperating with such prosecutions; and
(3) the Minister of Defense is making publicly available audits of receipts and
expenditures of the Indonesian Armed Forces, including audits of receipts from
private enterprises and foundations.
FY2004 Foreign Operations Appropriations (P.L. 108-199). For
FY2004 the Administration requested $132.1 million for all Indonesia programs
administered by the U.S. Agency for International Development, including P.L. 480,
Title II food aid, a decrease of $11.4 million from the $141.5 million allocated for
In December 2003, the Foreign Operations bill, H.R. 2800, was wrapped into
the omnibus Consolidated Appropriations Act, 2004 H.R. 2673 which became law
in January 2004 (P.L. 108-199). The act contains language on Indonesia that places
certain limitations on assistance to Indonesia. Specifically, section 597 allows FMF
funds to be expended, and licences for the export of lethal defense articles to be
issued, only if the President certifies to Congress that the TNI is actively suspending,
prosecuting, and punishing those responsible for human rights abuses and that the
TNI is cooperating with the United Nations East Timor Serious Crimes Unit and that
the Minister of Defense is making publically available audits of TNI’s accounts.
IMET is to be available for Indonesia if the Secretary of State reports to Congress
that Indonesia is cooperating with the Federal Bureau of Investigation’s investigation
of the attack on Americans at Timika. The act adds that such restrictions do not
apply to expanded IMET.
FY2005 Foreign Operations Appropriations (P.L. 108-447). Section
572 conditions Foreign Military Financing (FMF) of “lethal defense articles” to the
TNI to certification by the Secretary of State that the TNI is taking steps to counter
international terrorism, that the Indonesian government is prosecuting and punishing
TNI members guilty of human rights abuses or aiding militia groups, that the TNI is
cooperating with efforts to resolve cases of human rights abuses “in East Timor and
elsewhere,” and that the TNI is increasing transparency and accountability of their
financial assets and expenditures. An exception is made to these conditions by
Section 590, which allows FMF for the Indonesian navy for enhancing maritime
security. Section 572 also conditions Indonesian eligibility for participation in IMET
to certification by the Secretary of State that the Indonesian government and the TNI
are cooperating with the U.S. FBI’s investigation of the Timika attack and killings.
In February 2005, Secretary of State Condoleezza Rice determined that the
Indonesian government and armed forces (TNI) had cooperated with the FBI’s
investigation into the murders of two United States citizens and one Indonesian in
2002 in Timika, Papua province, thereby satisfying legislative conditions, and
certified the resumption of full IMET for Indonesia. In May 2005, the Bush
Administration resumed Foreign Military Sales (FMS) of nonlethal U.S. defense
articles which were needed in the Aceh relief effort.

FY2006 Foreign Operations Appropriations (P.L. 109-102). The
Foreign Operations, Export Financing, and Related Programs Appropriations Act,
2006 (P.L. 109-102), Section 599F(a), continued existing restrictions on FMF, stating
that such assistance may be made available for Indonesia only if the Secretary of
State certifies that the Indonesian government is prosecuting, punishing, and
resolving cases involving members of the Indonesian military (TNI) credibly alleged
to have committed gross violations of human rights in East Timor and elsewhere.
Notwithstanding section 599F(a), FMF may continue to be made available to the
Indonesian Navy to enhance maritime security. P.L. 109-102 also requires the
Secretary of State to report on the status of the investigation of the Timika murders
and on cooperation provided by the Indonesian government in the investigation.
Section 599F(b) provided that the Secretary of State may waive restrictions on FMF
for Indonesia if such action would be in the national security interests of the United
States. In November 2005, the Secretary of State waived restrictions on FMF to
Indonesia on national security grounds pursuant to Section 599F(b).

Appendix C: Maps

Figure 2. Southeast Asia

Figure 3. Indonesia


Figure 4. Malaysia and Singapore


Figure 5. The Philippines

Figure 6. Thailand