Terrorism in Southeast Asia

Terrorism in Southeast Asia
Updated July 2, 2008
Bruce Vaughn, Coordinator, Emma Chanlett-Avery,
Mark E. Manyin, Michael Martin, and Larry A. Niksch
Asian Affairs Section
Foreign Affairs, Defense, and Trade Division

Terrorism in Southeast Asia
Since September 2001, the United States has increased focus on radical Islamist
and terrorist groups in Southeast Asia, particularly those in the Philippines,
Indonesia, Malaysia, Thailand, and Singapore. Southeast Asia is a base for past,
current, and possibly future terrorist operations. Al Qaeda 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), which has had
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. Since the Bali bombing in 2002, which JI is suspected of carrying
out, crackdowns by various governments in the region — encouraged and in some
cases supported by the U.S. government and military — are believed to have severely
weakened the organization. Its ability and willingness to carry out attacks against
Western targets. JI, however, has not been eradicated.
To combat the threat, the U.S. has pressed countries in the region to arrest
suspected terrorist individuals and organizations, funded and trained Indonesia’s elite
counter-terrorist unit, and deployed troops to the southern Philippines to advise the
Philippine military in their fight against the violent Abu Sayyaf Group. It has also
launched a Regional Maritime Security Initiative to enhance security in the Straits of
Malacca, increased intelligence sharing operations, restarted military-military
relations with Indonesia, and provided or requested from Congress substantial aid for
Indonesia and the Philippines. Also, since 2001, Thailand and the United States have
substantially increased their anti-terrorism cooperation.
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 its citizens. 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 Muslim insurgency in southern Thailand has escalated
in recent years as has terrorist activity in southern areas of the Philippines.
The report looks at the rise of Islamist militancy and the JI network before
discussing terrorism in the region and concludes with a section on options for U.S.
policy. Strategies include placing greater emphasis on attacking the institutions that
support terrorism, building up regional governments’ capacities for combating
terrorist groups, and reducing the sense of alienation among Muslim citizens.

The Rise of Islamist Militancy in Southeast Asia.........................1
Overview ....................................................1
The Rise of Al Qaeda in Southeast Asia............................3
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 ..................................................9
Indonesia .......................................................10
Recent Events................................................10
Trial of JI leaders.........................................11
JI Outlawed by Court......................................12
Political Extremism and Violence in Indonesia..................12
Background .................................................13
The Bali Bombings and Other JI attacks in Indonesia ................15
The Trial and Release of Baasyir ................................17
U.S.-Indonesia Cooperation.....................................18
The Philippines..................................................18
Abu Sayyaf..................................................18
The MILF...................................................19
The Philippine Communist Party (CPP) ..........................20
U.S. Support for Philippine Military Operations.....................20
Thailand ........................................................21
Southern Insurgency...........................................22
Thaksin and Surayud’s Approaches...........................22
Current Government’s Approach.............................23
Little Evidence of Transnational Elements.....................24
Leadership of Insurgency Unclear............................24
U.S.-Thai Cooperation.........................................24
Malaysia ........................................................25
Recent Events ...............................................26
Background .................................................27
A Muslim Voice of Moderation..............................27
Maritime Concerns........................................28
U.S.-Malaysia Counter-Terrorism Cooperation .....................28
Terrorism and Counter-Terrorism in Malaysia......................29
Singapore .......................................................31
U.S.- Singapore Cooperation ...................................31
Enhanced Homeland Security ..................................31
Options and Implications for U.S. Policy..............................32

Other Policy Implications ......................................34

Terrorism in Southeast Asia
The Rise of Islamist Militancy in Southeast Asia
While there has been significant anti-Western terrorist activity in Southeast
Asia, counter-terror measures in recent years appear to have significantly degraded
anti-Western terrorist groups’ ability to launch attacks against Western targets in the
region. 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. 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. In pursuit of these objectives, they have planned
and carried out violent attacks against American and other Western targets as well
as against Southeast Asian targets. 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. 1
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 concern 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 Muslims’ perceptions of America’s stance on the Israeli-Palestinian
conflict as “blatantly pro-Israel” makes it even more difficult for most governments

1 For the purposes of this report, Islamic refers to that which pertains to Islam in general
while the term Islamist connotes a concept that advocates a more strict interpretation of
Islam and a willingness to push a political and social agenda to implement Islamic law.
Distinctions are also drawn between those radicals and extremists who would advocate an
Islamist agenda through the political process and those terrorists and militants who would
also use violence, or the threat of violence, to promote such a cause.

to countenance an overt U.S. role in their internal security.2 The U.S. foreign policy
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.
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.
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 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 to operate. In recent years
Indonesian counter-terror efforts have been successful and appear to have
significantly curtailed JI operations.
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). Several Muslim extremist groups in the Philippines have focused their
operations in the relatively isolated Muslim-majority regions in the South.
The southern Thailand provinces of Pattani, Yala, Narathiwat, and part of
Songhkla were once part of an independent sultanate. After Thailand (then called
Siam) incorporated the provinces in 1902, a series of central government-directed
assimilation policies were instituted, which has inspired varying degrees of resistance
from the ethnic Malay Muslims, many of whom have sought to preserve their own
identity. By the late 1960s, a number of armed separatist groups had formed, but
attempts to forge a broad coalition of resistance failed. In 1981, Bangkok revamped
its approach to the South, emphasizing economic development and public
participation in governance, and encouraging hundreds of fighters to accept political
amnesty. The shift was largely successful and armed movements weakened, although
residual groups became more radicalized and continued guerilla activities. Through
the 1990s, Muslim political participation increased and violence declined
significantly. However, since 2004, sectarian violence has surged in the southern

2 Daljit Singh,”The Terrorist Threat in Southeast Asia,” in Russell Heng and Denis Hew,
eds., Regional Outlook, 2003-2004 (Singapore: Institute of Southeast Asian Studies, 2003).

In contrast to its neighboring nations, Malaysia does not currently have a
significant indigenous separatist group engaging in violent actions against the public.
While Malaysia has been used a gathering point for members of various terrorist
organizations, it has been relatively free of the terrorist attacks that have troubled
other Southeast Asian nations. Although there are political parties and people within
Malaysia who support the creation of a more conservative Islamic government in
Malaysia, the self-identified “moderate Muslim” nation has a history of comparative
religious tolerance and a rejection of violence done by so-called Islamic
fundamentalists. At the same time, the Malaysian government has been a staunch
critic of rhetoric that conflates terrorism with Islamic fundamentalism, which it sees
as being anti-Islam.
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.
Southeast Asian terrorist and militant groups can be placed on a spectrum that
spans the relatively narrow goals and objectives of the separatist Muslims in
Southern Thailand or Southern Philippines to the global anti-Western agenda of Al
Qaeda. In between can be placed groups such as JI, that has an internal debate over
the relative emphasis on achieving an Islamist agenda within individual states as
opposed to focusing their fight directly against Western targets. These groups, as well
as others such as the Abu Sayyaf Group, will be explored in greater detail below.
The Rise of Al Qaeda in Southeast Asia
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 loose
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” plot), 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.3 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.4 Al Qaeda’s leadership also has taken advantage of
Southeast Asia’s generally loose financial controls to use various countries in the
region as places to raise, transmit, and launder the network’s funds. By 2002,
according to expert opinion on Al Qaeda, roughly one-fifth of Al Qaeda’s
organizational strength was centered in Southeast Asia.5
Second, over time, Al Qaeda Southeast Asian operatives helped create what may
be Southeast Asia’s first indigenous regional terrorist network, Jemaah Islamiyah
(JI), which has plotted attacks against Western targets. Jemaah Islamiyah is believed
to have carried 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 2000.6 Al Qaeda operatives’ task was made easier by several
factors including 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 weak central government control. Other
factors included endemic corruption, porous borders, minimal visa requirements,

3 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, pp. 147-148.
4 For examples of how the September 11 plot organizers traveled relatively freely throughout
Southeast Asia to hold meetings and observe flight and airline employees’ patterns, see The

9/11 Commission Report, pp. 156-160.

5 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.
6 Zachary Abuza, “Terrorism in Southeast Asia,” in Strategic Asia 2002-2003 (Seattle, WA:
National Bureau of Asian Research, 2003).

extensive networks of Islamic charities, and lax financial controls of some countries,
most notably Indonesia and the Philippines.7
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, 2001 terrorist attacks, the full extent of the
pan-Asian terrorist network with extensive links to Al Qaeda was uncovered. The
network, known as Jemaah Islamiyah (Islamic Group), was discovered to have cells
in Indonesia, Malaysia, the Philippines, Singapore, and Thailand as well as in
Australia and Pakistan. Since the Bali bombing in 2002, which JI is suspected of
carrying out, crackdowns by various governments in the region are believed to have
severely weakened the organization.
Arrests and killings by Indonesian authorities in 2007 are thought to have been
particularly effective. Some analysts now believe JI is no longer a regional
organization, in that its administrative structure appears to be confined to Indonesia.
Even there, JI apparently was unable to muster forces to combat a January 2007
crackdown by police in the Central Sulawesi district of Poso that appears to have
driven JI from the area. JI’s links to Al Qaeda reportedly have withered. Most
analysts caution, however, that individual JI members remain scattered across the
region, are highly trained, and are capable of carrying out acts of violence.
Additionally, JI’s more moderate factions appear to have refocused on grass-roots
education, indoctrination, and other activities they feel are better suited to their long-8
term goal of instituting sharia law in Indonesia.
JI’s goals have ranged from establishing an Islamic regime in Indonesia, to
establishing an Islamic caliphate over Muslim regions of Southeast Asia and northern
Australia, to waging jihad against the West. Until the more militant factions either
were eliminated or broke away from the organization in the 2005-2007 period, there
appears to have been considerable debate within the organization about which of
these goals to pursue and prioritize, with different JI factions preferring different
objectives. Jemaah Islamiyah leaders have formed alliances with other militant

7 Zachary Abuza, Militant Islam in Southeast Asia: Crucible of Terror (Boulder: Lynne
Rienner Publishers, 2003).
8 “Southeast Asia,” Jane’s Sentinel Security Assessment, March 5, 2008; International Crisis
Group, “Indonesia: Tackling Radicalism in Poso,” Policy Briefing, Asia Briefing N°75, 22
January 22, 2008; Eric Schmitt, “Southeast Asia Sees Gains against Insurgencies,”
International Herald Tribune, June 9, 2008; Greg Sheridan, “Jakarta’s Terrorist Rehab,”
The Australian, May 31, 2008.

Islamist groups to share resources for training, arms procurement, financial
assistance, and to promote cooperation in carrying out attacks.
Indeed, there is some evidence that such cooperation increased after 2002, when
arrests and other counterterror actions began to take its toll on JI, forcing it to adapt
and form closer working relationships with other groups. Within Indonesia, some in
the network have created and/or trained local radical Islamist groups that have been
involved in sectarian conflict in the country’s outer islands. Additionally, there is
considerable evidence that JI has engaged in joint operations and training with
Filipino groups. For a time, JI’s main partner in the Philippines reportedly was the
separatist group, the Moro Islamic Liberation Front (MILF). There is growing
cooperation among the Abu Sayyaf Group, several major MILF commands, and
elements of JI on Mindanao and some JI members appear to have made Mindanao
a primary base of operations.
In October 2002, the United States designated JI as a foreign terrorist
organization. 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 are credited to more extensive intelligence sharing
among national police forces.
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
to 1965. 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.
The fall of Indonesia’s Suharto regime in 1998 provided a major boost to JI.9
Almost overnight, formerly restricted Muslim groups from across the spectrum were
able to operate. Baasyir and Sungkar returned to Solo, preaching and organizing in

9 For more information on Indonesia see CRS Report RL32394, Indonesia: Domestic
Politics, Strategic Dynamics, and American Interests, by Bruce Vaughn.

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 mujahideen fighters to
participate in the sectarian conflict, in which hundreds died.10 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, reports — 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.11 Whereas Al
Qaeda’s focus is global and definitively targets the West, Jemaah Islamiyah is
focused on radicalizing Muslim Southeast Asia (starting with Indonesia) and some
JI leaders are said to feel that attacking Western targets will undermine this goal.
After the arrests, deaths, defections, and/or marginalization of more militant
members in the middle part of the decade, JI’s known links to Al Qaeda reportedly
have dwindled to almost nothing.12
That said, the two networks have developed a highly symbiotic relationship.
There is reportedly some overlap in membership. They have shared training camps
in Pakistan, Afghanistan, and Mindanao. Al Qaeda has provided JI with considerable
financial support.13 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.14 The two networks have jointly planned operations — including the
September 11 attacks — and reportedly have conducted attacks in Southeast Asia
jointly.15 Often, these operations took the form of Al Qaeda’s providing funding and

10 Sidney Jones, “Indonesia Backgrounder: Jihad in Central Sulawesi,” International Crisis
Group Report No74, February 3, 2004.
11 Zachary Abuza, “Funding Terrorism in Southeast Asia: The Financial Network of Al
Qaeda and Jemaah Islamiyah,” NBR Analysis, December 2003, pp. 11-12; The 9/11
Commission Report, pp. 150-152.
12 Eric Schmitt, “Southeast Asia Sees Gains against Insurgencies,” International Herald
Tribune, June 9, 2008.
13 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.
14 The 9/11 Commission Report, p. 151. Yazid Sufaat is the individual JI sent to Kandahar.
15 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

technical expertise, while JI procured local materials (such as bomb-making
materials) and located operatives.16 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, was closest between 1997 and 2002.17
Jemaah Islamiyah’s Size and Structure
The total number of core Jemaah Islamiyah members at its peak was estimated
to range from 500 to several thousand.18 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.
Interrogations of Jemaah Islamiyah members have revealed a highly formalized
command structure, at least during the early part of the decade. JI was led in 2000-
2001 by a five-member Regional Advisory Council chaired by Hambali. 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. Each mantiqi,
in turn, was subdivided into at least three additional layers: battalions, platoons, and
squads. 19
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
another. 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. Finally, JI’s structure has expanded and contracted in response to
internal and external developments. Indonesian expert Sidney Jones has written that

15 (...continued)
16 The 9/11 Commission Report, p. 151.
17 Sidney Jones, “The Changing Nature of Jemaah Islamiya,” Australian Journal of
International Affairs, June 2005.
18 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.
19 Jones, “Jemaah Islamiyah in South East Asia,” pp. 27-28.

since 2002, a more flexible structure, “better suited for an organization under siege,”
undoubtedly has evolved.20
The breakdown of JI’s hierarchy also may have been exacerbated by tensions
between two factions over the best means for waging jihad, though it is unclear
whether the differences are over tactics or overall strategy. A minority group, led by
Hambali until his capture, is interested in focusing on a broader anti-Western agenda
similar to al Qaeda, and in effecting change in the near term. A leading JI operative
still at large, Noordin Muhammad Top, is believed to lead a splinter cell pursuing
this strategy. Opposing this faction is a majority group within JI, depicted as the
“bureaucrats,” that sees the anti-western focused militants’ 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 in the
future.21 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.22 The implication
is that JI may not be as monolithic as commonly assumed.23
Major Plots
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 Al Qaeda’s involvement in the plot. Follow-on
arrests netted plotters in Malaysia and the Philippines. The JI cell in Malaysia
reportedly coordinated the plot, including the procurement of bomb-making
materials, preparing forged travel documents, and communications with Al Qaeda.
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, 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

20 Jones, “The Changing Nature of Jemaah Islamiya,” p. 170.
21 Jones, “Jihad in Central Sulawesi,” pp. 24-25. The 9/11 Commission Report (note 26 on
p.490) notes that during his interrogation, Khalid Sheikh Mohammed said that 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.
22 Jones, “The Changing Nature of Jemaah Islamiya,” pp. 171-172.
23 International Crisis Group, Jihadism in Indonesia, Asia Report 127, January 24, 2007.

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 first anniversary of the September 11
attacks.24 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. In July 2005, Al-Farouq
and other suspected Al Qaeda members escaped from a U.S. military detention center
in Bagram, Afghanistan. In September 2006, he was killed in Basra, Iraq, during a
shootout with British troops.25 (See the Indonesia section below for more
information on the Bali bombings and other attacks in Indonesia.)
Recent Events
JI has not carried out a large-scale anti-Western attack in Indonesia since the
second Bali bombing of October 2005. This has been interpreted as a sign of JI’s
degraded operational capability. The United States lifted its travel warning on
Indonesia in May 2008. U.S. Ambassador to Indonesia Cameron Hume stated that
the warning, which was first issued in November 2000, was lifted due to “objective
improvements made by Indonesia in its current security situation.”26
Indonesian authorities believe they have seriously damaged JI and its ability to
carry out large scale attacks. Detachment 88 is the Indonesian national police force’s
main counter-terror unit and is thought responsible for much of the success that
Indonesia has had in arresting hundreds suspects of which many have been tried and
convicted. In May 2008, an associate of Noordin Top, Faiz Fauzan, was apprehended
by Indonesian authorities. Fauzan is thought to have had a role in the Bali bombing
of 2005.27 JI was also declared an illegal organization by an Indonesian judge in a
terrorism trial in April of 2008.28 Indonesia has also apparently had success through
its program of deradicalisation which seeks to bring both the extremist and their

24 Romesh Ratnesar, “Confessions of an Al-Qaeda Terrorist,” Time, September 23, 2002.
25 Eric Schmidt and Time Golden, “Details Emerge on a Brazen Escape in Afghanistan,”
New York Times, December 4, 2005; “Profile: Omar al-Farouq,” BBC News, September 26,


26 Tanja Vestergaard, “U.S. Drops Indonesia Travel Warning as Security Situation
Improves,” Global Insight, May 26, 2008.
27 “Indonesia Arrests Alleged Bali Bomb Plotter,” Agence France Presse, May 5, 2008.
28 Hamish McDonald, “Fighting Terrorism with Smart Weaponry,” The Sydney Morning
Herald, May 31, 2008.

families back into the fold of normal society in addition to preventing, deterring, and
punishing terrorists.29
U.S. Attorney General Michael Mukasey praised Indonesia’s efforts in
combating terrorism during a visit to Jakarta in June 2008.
Like Indonesia, the United States has faced terrorist threats and terrorist attacks.
We share the challenge of combating violent extremists, while protecting basic
civil liberties in the process. Indonesia has been effective in the apprehension and30
conviction of terrorists and extremists organizations.
In March 2008, Acting Director of the National Counterterrorism Center Michael
Leiter stated “Southeast Asia continues to be a concern, although not nearly that
which we might have envisioned two or three years ago.”31
Indonesia also has strong bilateral counter-terror cooperation with Australia and
it appears that this will continue under the leadership of the new Australian Prime
Minister Kevin Rudd. During a June 2008 visit to Indonesia, Rudd stated that he and
President Yudhoyono agreed to expand security cooperation within the framework
of the Lombok Treaty of 2006. He stated “... we’ve responded [to terrorist attacks]
by strong practical cooperation preventing terrorism and tracking down the
perpetrators ... I want to pay special tribute to the close cooperation we have in this
area ... The government that I lead is committed to maintaining and strengthening
that security cooperation.”32
Trial of JI leaders. An Indonesian court handed out 15-year sentences to Abu
Dujana and Zarkasih in April 2008. The two JI leaders were captured in June 2007.
Zarkasih was JI head for Mantique II and was thought to be the defacto head of JI
since 2004. Abu Dujana was head of JI’s military wing. They were convicted for
harboring terrorists and on firearms charges. Dujana was convicted for harboring
Muhammad Top who is thought to be one of the leaders behind the Bali bombing
who has yet to be captured.33 Some believe Top may have fled Indonesia.34 Their
sentencing is viewed as a key success for Indonesia’s counter-terror effort.35 Dujana
is thought to have had a role in the Marriott bombing, the Jakarta Australian Embassy
bombing, and the 2002 Bali bombing.

29 Greg Sheridan, “Jakarta’s Terrorist Rehab,” The Australian, May 31, 2008.
30 “United States/Indonesia: US, Indonesia Combine Efforts to Fight Transnational Crime,
Terrorism,” Thai News Service, June 11, 2008.
31 Eric Schmitt, “Southeast Asia Sees Gains Against Insurgencies Fighting Terrorism,” The
New York Times, June 9, 2008.
32 “Australian PM in Indonesia for Talks on Security, Environment,” Voice of America, June

13, 2008.

33 “Indonesia Jails Leaders of ‘Terrorist’ JI,” SBS News, April 22, 2008.
34 “Wanted Terror Suspect May Have Fled Indonesia,” The Wall Street Journal, May 20,


35 Tanja Vestergaard, “Leaders of Indonesia’s Terrorist Group JI Handed 15-Year
Sentences,” Global Insight, April 22, 2008.

JI Outlawed by Court. The South Jakarta District Court that sentenced Abu
Dujana and Zarkasih declared JI a “forbidden corporation” for the first time and
found it guilty of being an organization that permits terrorism. It is thought by some
that this move will have significant ramifications for Indonesia’s fight against36
terrorism in Indonesia. The lead judge in Abu Dujana’s trial, Judge Wachyono,
described JI as a “terrorist organization.”37 Australian Foreign Minister Stephen
Smith is reported as stating that Indonesia has convicted over 180 terrorists in the
past six years.38 Terrorist expert Rohan Gunaratna is reported to have stated that the
court ruling enables Indonesian authorities to re-arrest JI’s co-founder Abu Bakar
Baasyir, who served a 1 ½-year jail term for helping to plan the 2002 Bali39
There are differences of opinion on just what the court’s move will mean. It is
apparently understood by some to mean that the police can arrest anyone belonging
to JI, though many leaders of JI, and others, have denied the group exists. The Vice
President, Jusuf Kalla has also reportedly stated “Jamaah Islamiyah does not exist as40
an organization and therefore it cannot be banned.” Without a government ban,
arrests could be challenged in the courts.41 Former Australian Office of National
Assessments analyst Ken Ward is reported as stating that “A court simply hasn’t the
jurisdiction to declare an organization illegal; that has to be done by the42
government.” Zachary Abuza, an expert on Southeast Asian terrorism, reportedly
stated that the impact of the ruling is unclear and that parliament must endorse it or43
it will leave the authorities fighting JI “with one arm tied behind their back.”
Nevertheless, the court’s move is viewed as a positive step in Indonesia’s ability to
combat terrorism.
Political Extremism and Violence in Indonesia. Violence and fear
continue to be used by radical Islamists to try to coerce the Indonesian government
to change policy to facilitate an Islamist agenda. Members of the Front Pembela
Islam (FPI), or Islamic Defenders Front (IDF), attacked a group of peaceful
demonstrators on June 1, 2008, who were demonstrating at The National Monument
in Jakarta in support of tolerance and moderation regarding efforts by Muslim
hardliners to have the Ahmadiyah sect banned in Indonesia. Ahmadiyah believe
Mohammad was a prophet but not the last one. As such, their beliefs are inconsistent
with the beliefs of other Muslims. The police were reportedly reluctant to intervene

36 “Smith Welcomes Court Move Against JI,” Australian Associated Press, April22, 2008.
37 “Indonesia Jails Leaders of ‘Terrorist’ JI,” SBS News, April 22, 2008.
38 “Smith Welcomes Indon Court Move Against JI,” Australian Associated Press, April 22,


39 Mark Forbes, “Heavy Blow to JI as Terror Group Declared ‘Forbidden’,” The Age, April

22, 2008.

40 “JI Does Not Exist, Vice President Says,” The Jakarta Post, May 3, 2008.
41 Mark Forbes, “JI Declared an Illegal Network,” The Sydney Morning Herald, April22,


42 Daniel Flitton, “Court Directive on JI Hollow,” The Age, April 25, 2008.
43 Mark Forbes, “The Fading Power of JI,” The Age, April 25, 2008.

to stop the June 1 attacks despite reportedly being present in large numbers.
Following the attack IDF leader Habib Rizieq called on his followers to “prepare for
war with Ahmadiyah and its followers” unless a ban was enacted by the
government. 44
Several days after the attack the government reacted to Indonesian moderates’
outrage by arresting members of the FPI but also bowed to pressure from extremists
and placed a partial ban on the Ahmadiyah. Observers believe this demonstrates that
the government remains somewhat reluctant to alienate hardline Muslims and will
act to placate them. Some have expressed concern that a message that may be
conveyed is that extremists can advance their cause through violence. It is also worth
noting that the government reacted to address in part moderate concerns with the
incident by arresting FPI members responsible for the violence.45
While inter-communal violence elsewhere in Indonesia has been significantly
reduced in recent years, there are signs that inter-communal violence between
Christians and Muslims could erupt in Papua. A June 2008 International Crisis Group
report stated “violence was narrowly averted in Manokwari and Kaimana in West
Papua Province in 2007, but bitterness remains.” Dispute over plans developed in
2005 to build a Mosque on the site where German Missionaries brought Christianity
to Papua in the 19th century has angered the Papuan Christian community. It also
appears that this religious fault line is related to ongoing migration of Muslims to
Papua and West Papua from elsewhere in Indonesia.46 Indonesia’s recent history has
demonstrated that Islamist extremists and terrorists have used inter-communal strife
in the past, in places such as Ambon and Poso in the Malukus and on Sulawesi, as
a means of mobilizing support for their cause and as a way of recruiting members.
In August 2007, Indonesian President Susilo Bambang Yudhoyono in his State
of the Union address stated “the acts of terrorism that have caused unrest in our
society in the past years have been handled.... We have succeeded in preventing and
tackling the acts of terrorism in the country.” He went on to add that more needs to
be done to address the root causes of terrorism including “poverty, injustice,
extremism, and a culture of violence.”47 His statement follows the June 2007 capture
of JI Emir Zarkarsih and JI military leader Abu Dujana. In his speech, Yudhoyono
stated that the security situation in Sulawesii and the Malukus had improved.

44 Stephen Fitzpatrick, “We’ll Wage War: Muslim Hardliners,” The Australian, June 3,


45 Julia Suryakusuma, “Zero Tolerance for Bullies and Thugs,” The Straits Times, June 12,


46 “Indonesia: Communal Tensions in Papua,” International Crisis Report No 154, June 16,


47 “Indonesia’s president Claims Victory in war Against Terror,” DowJones Newswire,
August 16, 2007.

Others caution that although much has been done to neutralize JI a core element
of some 900 militants, including 15 first generation militants, remain at large and that
they retain the capacity to mount attacks. International Crisis Group expert Sidney
Jones doubts that any terrorist group in Indonesia has the capacity to mount a major
attack, but is of the opinion that JI has the ability to recruit new members and to
regenerate. “You can’t fully eradicate the problem. But you can put in place
institutions, information-sharing mechanisms and various controls ... to reduce the
scope of threats,” Jones has said.48 Paul O’Sullivan, Director General of the
Australian Secret Intelligence Organization (ASIO), has stated that “successful
counter-terrorism efforts by Indonesian authorities have eroded JI’s capabilities but
Noordin Muhammad Top remains at large, and there is no room for complacency.”
(See below for more information on Noordin Top.) He added that “terrorism around
the globe is likely to be a destabilizing force for the next generation.”49
Statements by captured JI leader Abu Dujana have been interpreted by some to
confirm that there has been a split in JI between those within the organization who
would focus on attacking Western targets, which would include Noordin Top’s
splinter cell, and those who wish to focus their activities on effecting change in
Indonesia. Though success by the Indonesian government does appear to have
significantly disrupted JI organization and degraded JI capabilities in Indonesia, JI
does not appear to have been eliminated, and may yet regroup and conduct further
operations in Indonesia in the future.50 To address this, some analysts have cautioned
policy makers against complacency and urged further effort to deny loosely governed
regions, particularly in Mindanao in the Philippines and Southern Thailand in
Southeast Asia from being used by terrorist groups.51
Indonesia’s attractiveness to Islamist terrorist groups appears to derive primarily
from relatively weak central government control and considerable social and political
instability and its overwhelmingly Muslim population. Indonesia’s central
government was weakened by the 1997-1999 Asian financial crisis. 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 weakened its
ability to marginalize Islamist elements within Indonesian society. Indonesia’s
former President Megawati Sukarnoputri, 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 campaigns in
Afghanistan and Iraq.52 The election of Susilo Bambang Yudhoyono in 2004 has led
the Indonesian central government to be both more assertive and more effective in
its counterterrorist activities. Muslim-Christian strife in the country’s remote regions

48 “Leaders Shouldn’t Let Terrorism Slip from APEC Agenda-Experts,” DowJones
Newswire, September 3, 2007.
49 Doug Conway, “Warning of Terror to Come,” The Courier Mail, June 21, 2007.
50 “Dujana Admits Bakar was JI Spiritual Leader,” SBS, June 27, 2007.
51 Stephen Coates, “SE Terror Groups Pose ‘Very Real’ Threat: Think Tank,” Agence
France Presse, June 25, 2008.
52 Richard Paddock, “Indonesia Presses U.S. to Stop Bombing Asia,” Los Angeles Times,
November 2, 2001.

has attracted the involvement of foreign Islamist 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. The as yet unresolved tension
between Christian and Muslim communities in Sulawesi and the Malukus offers
terrorists a conflict that they may be able to manipulate to further their ends.53
Even the more extreme groups traditionally have been concerned primarily with
domestic issues such as promoting the adoption of Islamic law (sharia). Only a small
minority of the Muslim parties favor Islamist agendas. A 2007 Pew Research Poll
found that support for suicide bombings and other forms of violence against civilians
in defense of Islam had dropped significantly in Indonesia in recent months.54 The
U.S.-led campaign against terrorism and the war in Iraq have had negative political
resonance in Indonesia. While 95% of Indonesians support religious tolerance, about
3% still support bombings and attacks against non-Muslims.55 Although a small
percentage, this equates to a large number of individuals in a nation of some 235
million people.
The Bali Bombings and Other JI attacks in Indonesia
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
terrorist attack since the September 11, 2001 attacks in the United States, appeared
to mark a shift in JI’s strategy; the FBI reported that in early 2002, senior JI leaders
— meeting in Thailand — decided to attack “softer targets” in Asia such as tourist
sites frequented by Westerners.56 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

53 “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.
54 “Support Declines Among Muslims for Violent Defense of Islam,” Radio Free Europe,
July 26, 2007.
55 Mark Forbes, “JI Openly Recruits as Leaders Quizzed,” The Age, June 23, 2007.
56 Jay Solomon and James Hookway, “Bali Bomb Suspect Used Thailand as Staging Area,”
The Wall Street Journal, November 7, 2002.

100 injured, including two Americans and other Westerners, when three suicide
bombers attacked restaurants frequented by foreigners.57
The 2002 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.58 With the substantial aid of Australian and U.S.
investigators, Indonesian police 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.
Other bombings believed to have been carried out by JI since 2002 include the
bombing of the Marriott Hotel in Jakarta in August 2003 that killed more than ten
people and injured dozens; the bombing of the Australian Embassy in September

2004, killing 10 and wounding around 200; and the Bali II bombing of October 2005,

in which three suicide bombers exploded bombs within minutes of one another in
Bali, killing more than 20 people and wounding more than 100. All of the attacks are
believed to have been planned by Noordin Muhammad Top. Most of the victims
have been Indonesians.
Noordin Muhammad Top, a Malaysian, has been the target of a large manhunt
by Indonesian police for his suspected role of strategist for JI’s major bombings.
Muhammad Top’s base of recruits appears to be drawn from like-minded operatives
from JI and increasingly from other militant Islamist groups in Indonesia, such as
those involved in sectarian violence in the Malukus and Poso, and the Philippines.
By 2005, according to some sources, Noordin Top was declaring himself the leader
of Al Qaeda for the Malay Archipelago. Many of the more “mainstream” JI members
reportedly consider Noordin as a danger to the future of the organization.59
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 in Poso. Reportedly many of
these incidents have involved elements of JI as well as offshoots of Darul Islam and
Kompak. This is because many of the militants see areas as the most likely sites 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

57 R. Pura and L. Lopez, “Bali Blast Signals Militants Rebirth,” The Wall Street Journal,
October 3, 2005.
58 Ellen Nakashima and Alan Sipress, “Al Qaeda Linked to Blast by Official,” Washington
Post, October 15, 2002.
59 See, for instance, International Crisis Group, Terrorism in Indonesia: Noordin’s
Networks, Asia Report 114, May 5, 2006; “Profile, Noordin Muhammad Top,” Jane’s
Terrorism & Security Monitor, November 15, 2006.

of an Islamic state.”60 The increased militant activity in Maluku and Poso in 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.61
The Trial and Release of Baasyir
The Bali bombing 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 Sukarnoputri
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 2001.62
On September 3, 2003, an Indonesian court convicted him of plotting to
overthrow the Indonesian government. 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.63
As the trial against Baasyir proceeded it appeared that the prosecution had a
relatively weak case. This may have been the result of the prosecution’s inability to
get key witnesses to testify against Baasyir.64 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.65 Only
one witness testified that Baasyir was the leader of JI.66
The prosecution called for only a reduced sentence of eight years in jail instead
of the death penalty. Baasyir was sentenced to 30 months’ imprisonment for

60 “Weakening Indonesia’s Mujahidin Networks: Lessons from Maluku and Poso,”
International Crisis Group, October 13, 2005.
61 Sidney Jones, “Asking the Right Questions to Fight Terror,” The Jakarta Post, January

9, 2006.

62 Abuza, “Tentacles of Terror,” p. 72.
63 Raymond Bonner, “U.S. Pressure to Hold Militant Sets Off Outcry in Indonesia,” New
York Times, April 20, 2004.
64 “Bashir: A Strong Chance to walk Free,” Australian Associated Press, February 9, 2005.
65 Sian Powell, “Call for Baasyir Jail Term,” The Australian, February 9, 2005.
66 “Indonesian Prosecutors Ask for Eight-Year Jail Sentence for Bashir,” Voice of America,
February 8, 2005.

conspiracy in the 2002 Bali bombings in April 2004. His sentence was reduced in
August 2005 by four months and 15 days. He was released in June 2006, and in
December 2006 an Indonesian judge overturned his conviction.
Since his release Bassyir has traveled and preached openly in Indonesia. He has
continued to call for the implementation of sharia law, to state that democracy and
Islam are incompatible, and to say that Muslims should resist U.S. and Western
influence.67 He has also called for Indonesia’s anti-terror unit, Detachment 88, to be
disbanded claiming that it is a tool of the United States to stigmatize Islam.68
U.S.-Indonesia Cooperation
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.69
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, making the Philippines
one of the most extensive examples of U.S. counterterrorism cooperation in
Southeast Asia.
Abu Sayyaf
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

67 See, for instance, Michael Sheridan, “Bali Terror Chief’s New Mission,” The Sunday
Times, August 2006.
68 Mark Forbes, “West Funds Elite Unit to Destroy Islam,” The Sydney Morning Herald,
June 27, 2007.
69 State Department, Office of the Spokesman, Washington, DC, “Taken Question at Daily
Press Briefing,” January 4, 2006. Eric John, “U.S. and RI: A Strategic Partnership,” The
Jakarta Post, January 3, 2006.

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.
Under pressure from U.S.-supported Philippine military operations since 2002,
Abu Sayyaf’s armed strength has declined from an estimated 1,000 to 200-300. It
continued to operate in the Sulu islands south of Basilan and on the western
Mindanao mainland. Abu Sayyaf has ties with military factions of the Moro Islamic
Liberation Front (MILF) and JI. Abu Sayyaf and JI reportedly engage in joint
training with emphasis on training in bomb-making and planning urban bombings.70
By mid-2005, JI personnel reportedly had trained about 60 Abu Sayyaf cadre in bomb
assembling and detonations.71 Since 2003, Abu has carried out bombings and plotted
bombings in cooperation with JI and the MILF, including bombings in Manila.
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. 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.72 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.73
The MILF has had tenuous cease-fire agreements with the Philippine
government. The latest truce agreement was in June 2003. There has been a
substantial reduction in violence and armed clashes under the truce. A team of
international observers led by Malaysia began to monitor the cease-fire in October
2004. However, negotiations for a permanent settlement have stalemated over the
issue of the MILF’s proposal for the establishment of a “Bangsamoro” autonomous
state covering much of western Mindanao, the Sulu islands, and part of the island of
Palawan. At issue are the geographical configuration of the state, its political

70 Abuza, Zachary. Balik-Terrorism: The Return of the Abu Sayyaf. Carlisle, U.S. Army
War College, 2005, p. 27.
71 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.
72 John McBeth, “Across Borders,” Far Eastern Economic Review, July 22, 2004. p. 27.
73 Abuza, Balik-Terrorism: The Return of the Abu Sayyaf, pp. 14-19, 22-24.

authority in relation to the central government in Manila, and whether the Philippine
government will have to secure amendments to the 1987 Philippine constitution in
order to establish a Bangsamoro state. The outlook worsened in April 2008 when
Malaysia announced that it would withdraw from the international cease-fire
monitoring group. The Malaysian government criticized the Philippine government
for lack of flexibility in the negotiations with the MILF. Many observers express
concern that Malaysia’s withdraw could lead to a breakdown of the cease-fire.74
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
U.S. Support for Philippine Military Operations
The Bush Administration has supported the Philippine government’s policy of
applying military pressure on Abu Sayyaf and seeking a negotiated settlement with
the MILF. In 2002, the United States committed nearly 1,300 troops to the southern
Philippines to assist the Philippine armed forces (AFP) in operations against Abu
Sayyaf on the island of Basilan southwest of Mindanao. In 2005, the United States
committed about 450 troops to support two AFP operations. One has focused on
Abu Sayyaf in western Mindanao. The second has focused on the Sulu islands
southwest of Basilan, especially the island of Jolo, a longtime redoubt of Abu Sayyaf.
The U.S. role in all of these operations has been non-combat. It has involved
the provision of intelligence and communications support of the AFP, including the
employment of U.S. P-3 surveillance aircraft; deployment of Navy Seal and Special
Operations personnel with AFP ground units; joint training exercises with the AFP,
assistance to the AFP in planning operations; and conducting civic action projects75
with AFP to improve the lives of the local populace and turn it against Abu Sayyaf.
The U.S. Agency for International Development has concentrated U.S. aid projects

74 Patricio Diaz, Behind IMT pull-out: fingerpointing, MindaNews (internet), May 19, 2008.
Al Jacinto, Stalled GRP-MILF peace talks; MILF: we stand firm on self-determination,
Manila Times (internet version), May 4, 2008.
75 Raymond Bonner and Carlos Conde, U.S. and Philippines join forces to pursue terrorist
leader, New York Times, July 23, 2005, p. A4. James Hookway, Terror fight scores in
Philippines, Wall Street Journal Asia, June 20, 2007, p. 1. Roland Ramos and Inday Espina-
Varona, Expanded (old) war theater, Philippine Graphic, November 12, 2007, p. 14-18.

on Jolo and neighboring Tawi Tawi island as part of the $260 million in U.S. aid
committed to the southern Philippines since 2001.76
U.S. military support reportedly has achieved successes. AFP operations against
Abu Sayyaf have become more aggressive and effective on Basilan and Jolo. Abu
Sayyaf strength has been eroded to an estimated 200-300, and key commanders have
been killed. AFP commanders praised U.S. equipment, U.S. intelligence gathering,
and U.S. assistance in planning AFP operations. The U.S. military’s civic action
projects on Basilan and Jolo (medical treatment, water purification installations, farm
markets, renovation of schools) appear to have weakened support for Abu Sayyaf on
the islands.77
In supporting Philippine government-MILF negotiations, the Bush
Administration has stated that negotiations are the best means of de-linking the MILF
from Jemaah Islamiya and Abu Sayyaf.78 MILF leaders have asked the Bush
Administration to play a more direct role in its negotiations with the Philippine
government.79 However, if the Malaysian withdrawal from the cease-fire monitoring
group should lead to a breakdown of the cease-fire, the Bush Administration would
be confronted with difficult policy decisions regarding a possible U.S. role in a wider
war. The possibility of a clash between U.S. and MILF troops would increase. The
AFP could be expected to propose increased supplies of U.S. arms and military
equipment; and it likely would argue for a more direct U.S. military role. The
Philippine government might change its previous policy of opposition to a U.S.
military role against the MILF and encourage a U.S. military role at least similar to
the U.S. role in operations against Abu Sayyaf.
(See CRS Report RL33233, The Republic of the Philippines: Background and U.S.
Relations, by Thomas Lum and Larry A. Niksch; and CRS Report RL31265, Abu
Sayyaf: Target of Philippine-U.S. Anti-Terrorism Cooperation, by Larry Niksch.)
Thailand has endured a persistent separatist insurgency in its majority-Muslim
southern provinces, which includes the provinces of Yala, Narathiwat, Pattani, and
— to a lesser extent — Songhkla, while dealing with political instability in its

76 Fabio Scarpello, U.S. diplomat meets Philippines rebels amid ongoing controversy over
U.S. presence, AdnKronos International, February 28, 2008.
77 Simon Montlake, U.S. troops in Philippines defy old stereotype, Christian Science
Monitor, March 1, 2007, p. 7. Al Jacinto, U.S., Filipino troops go on charm offensive,
Manila Times (internet version), September 10, 2007.
78 Asia Security Monitor No. 147, November 2005. U.S. says peace deal in Manila may
pressure JI, Reuters News, October 22, 2005.
79 William M. Esposo, Who is the US supporting in the Mindanao war? Philippine Star
(internet), August 19, 2007.

capital.80 Since January 2004, sectarian violence between insurgents and security
forces in Thailand’s majority-Muslim provinces has left over 3,300 people dead
according to press reports. The groups that have led this surge in violence are
generally poorly understood, and their motives are difficult to characterize. Many
believe they are mostly focused on local autonomy, but even the Thai government
has poor understanding of the diverse groups active in the South.
Meanwhile, the government in Bangkok has undergone several political
transitions: a bloodless military coup in September 2006 ousted the
democratically-elected Prime Minister Thaksin Shinawatra, an interim government
took control for 15 months, and a new civilian government took power after elections
were held in December 2007. The successive administrations have taken somewhat
different approaches to curbing the violence in the south, but none appear to have
found a way to resolve the ongoing insurgency.
Southern Insurgency
The southern region 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. The death toll
of over 3,300 includes suspected insurgents killed by security forces, as well as
victims of the insurgents. This includes both Buddhist Thais, particularly monks and
teachers, and local Muslims.
After a series of apparently coordinated attacks by the insurgents in early 2004,
the central government declared martial law in the region. Moreover, 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 their arrest. The insurgents retaliated with a series of more
gruesome killings, including beheadings, following the Tak Bai incident.
Thaksin and Surayud’s Approaches. The Thaksin government’s handling
of the violence was widely criticized as ineffective and inflammatory. Critics charged
that the Thaksin Administration never put forth a sustained strategy to define and
address the problem, that it repeatedly and arbitrarily shuffled leadership positions
of those charged with overseeing the region, and that it failed to implement adequate
coordination between the many security and intelligence services on the ground.
Under the military government, interim Prime Minister Surayud Chulanont took a
more conciliatory approach by publicly apologizing to Muslim leaders for past
government policies in the South and resurrecting a civilian agency responsible for

80 For more information on political developments in Thailand, see CRS Report RL32593,
Thailand: Background and U.S. Relations, by Emma Chanlett-Avery.

improving relations between the security forces, the government, and southern
Muslims that Thaksin had abolished. General Sonthi Boonyaratglin, leader of the
coup and the first Muslim commander of the Army, advocated negotiations with the
separatist groups as opposed to the more confrontational strategy pursed by Thaksin.
However, the violence increased in the months following the coup.81 Some analysts
said that a younger generation of more radicalized insurgents resisted the more
conciliatory approach of the new leadership in Bangkok. Criticism emerged that
Surayud’s policies were insufficiently implemented, law enforcement was unable to
effectively prosecute cases, and that intelligence coordination remained abysmal.
Current Government’s Approach. The current government, under the
leadership of Prime Minister Samak Sundaravej, has claimed that the South is a
priority, but critics maintain that his administration has not focused adequate
resources on the area as it has struggled to maintain its hold on power in Bangkok.
The region remains under martial law, which allows security forces to arrest suspects
without warrants and detain them for up to 30 days. Since June 2007, a more
concentrated counter-insurgency campaign know as “Operation Southern Protection”
had led to far more arrests; many analysts see the mass arrests as fueling local
resentment. Daily violence had ebbed somewhat as a result of the military
crackdown, but observers note an increase in more lethal and bold attacks, including
a March 2008 car bombing of a prominent hotel in Pattani that is known for hosting
official delegations.82 The Samak government has announced that it will try and curb
the violence by encouraging investment in the region as the poverty rate has
increased and industries have shut down.83 Human rights groups have continued to
criticize the military for its mistreatment of Muslim suspects; in March 2008, Human
Rights Watch accused the army of torturing an arrested Muslim cleric who later died84
in police custody.
Close observers note that attacks have become more provocative, more deaths
are caused by increasingly powerful explosions, and the insurgents have directed
more attacks at economic targets, particularly those owned by ethnic Chinese. Some
analysts describe a movement increasingly driven by an Islamist agenda: the
insurgents appear intent on driving a harsher ideological line and labeling
conciliatory Muslims as collaborators. Because of the repeated attacks on state-run
schools, many citizens have chosen to send their children to private Islamic schools.
The insurgents’ village-level network has expanded, perhaps driving more local85
support. As the attacks have become more sophisticated and coordinated, a climate

81 “Thailand’s Leaders Struggle for Solution as Separatists’ Violence Increases,” The New
York Times. February 26, 2007.
82 “Insurgents Turn Up Heat with Hotel Blast,” South China Morning Post. March 22, 2008.
83 “Thailand to Encourage Investment in Restive South,” Dow Jones International News.
March 21, 2008.
84 “Thailand: Imam’s Killing Highlights Army Abuse in South,” from Human Rights Watch
webpage at [http://hrw.org/english/docs/2008/03/26/thaila18346.htm].
85 “Southern Thailand: The Impact of the Coup,” International Crisis Group. March 15,


of fear has developed and division along religious lines has accelerated. According
to some reports, 15% of the Buddhist population has left the region.86
Little Evidence of Transnational Elements. 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, and that the overall long-term
goal of the movement in the south remains the creation of an independent state with
Islamic governance. 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 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 incidents to forge alliances between local separatists and
regional Islamic militants. Some of the older insurgent organizations earlier were
linked to JI, have reportedly received financial support from foreign Islamic groups,
and have leaders who have trained in camps in Libya and Afghanistan. Despite these
links, foreign elements apparently have not engaged significantly in the violence.
Leadership of Insurgency Unclear. Identifying the groups directing the
insurgency has been challenging, but most analysis suggests that there is no one
organization with authority over the others. Some reports suggest that the Barisan
Revolusi Nasional-Coordinate (BRN-C) has coordinated other groups that operate
largely autonomously. Other actors are the older Islamist separatist groups the
Pattani United Liberation Organization (Pulo) and Gerakan Mujahideen Islam Pattani
(GMIP). In April 2008, a Pulo website claimed that its members were committed to
resolving the violence through a dialogue with the Thai government, but neither the
central government nor the other groups followed suit. An organization called
Bersatu at one point claimed to be an umbrella grouping for all the insurgent factions,
but appears to have very limited authority over the disparate networks. The failure
of the Thai government to establish an authority with whom to negotiate limits its
ability to resolve the conflict peacefully.
U.S.-Thai Cooperation
Part of the U.S. concern about Thailand’s vulnerability to international terrorism
stems from Thailand’s relatively lax border controls and tourist-friendly visa
requirements. 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, and laundering money. There have been 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 fled to
Thailand to escape arrest in other Southeast Asian countries.

86 Zach Abuza, “Wake Up Call,” e-newsletter. March 20, 2007.

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. According to press reports, the CTIC took the
lead in capturing Hambali and also has captured a number of other suspected JI
operatives, acting on CIA intelligence. Thailand also reportedly provided a black site
where U.S. CIA officials were allowed to secretly hold suspected terrorists.87
According to press reports, two major Al Qaeda figures captured in Pakistan were
flown to Thailand for interrogation by U.S. officials in 2002.
It is unclear to what extent U.S.-Thai counterterrorism cooperation was affected
by the U.S. response to the military coup in September 2006. Unspecified
counterterrorism funds appropriated under Section 1206 of the National Defense
Authorization Act for FY2006 were suspended, but other programs “deemed to be
in the U.S. interest” continued, according to the U.S. State Department. Regardless,
the State Department certified that Thailand had restored a democratically elected
government in February 2008, removing legal restrictions to providing assistance to
Unlike many of its neighbors in Southeast Asia, Malaysia has no indigenous
separatist groups or insurgents that are generally viewed as engaging in terrorist
activities. The purported terrorist groups that do remain in Malaysia are generally
external in nature, comparatively small and relatively inactive. Following the events
of September 11, 2001, Malaysia was briefly considered a “hot spot” for global
terrorism because some of plotters of the attacks reportedly met in Kuala Lumpur.
Since then, Malaysia has been largely out of the spotlight in the global counter-
terrorism efforts.
However, because Malaysia views itself as a prime example of a more moderate
Muslim nation, it believes it has a better understanding of the causes of and solutions
for terrorism than other nations. In particular, Malaysia has been one of the harshest
critics of the Bush Administration’s strategy for conducting the “global war on
terrorism.” During the administrations of its former Prime Minister Mahathir
Mohammed and its current Prime Minister Abdullah Badawi, Malaysia has
maintained that U.S. anti-terrorism policies and strategies are leading to the growth
— and not the decline — in the membership and popular support for so-called
“terrorist groups.”Instead, Malaysia has advocated an approach that focused on
combating what it sees as root causes of terrorism, such as poverty and the denial of
human rights.

87 “Thai War on Terrorism Presents Diplomatic Headache,” Sydney Morning Herald.
September 23, 2006.

Despite these sharp differences in their policies and strategies, Malaysia has
generally been supportive of specific U.S. counter-terrorism programs and initiatives
in Southeast Asia. In addition, certain aspects of Malaysia’s domestic counter-
terrorism policies are seen to mirror those in the United States. In some cases,
Malaysia’s domestic counter-terrorism programs have been sharply criticized for
needlessly curtaining civil liberties and providing the Abdullah administration with
tools to suppress political opposition.
Recent Events
Malaysian officials recently expressed concern that rising oil and food prices,
as well as the overall weakening of the global economy, might lead to a growth of
social unrest and terrorism. During the 8th ASEAN Senior Officials Meeting on
Transnational Crime (SOMTC), Malaysia’s Home Minister Syed Hamid Albar linked
the declining global economic situation to a potential rise in terrorism and other
forms of crime.88 The Home Minister’s views were reflected in the comments of
Prime Minister Abdullah during the July 2008 D8 meeting in Kuala Lumpur.89
Abdullah linked rising oil and food prices to a growing risk of “political unrest in
many societies.”90
On the operational side of its counter-terrorism efforts, Malaysian authorities
captured two JI operatives in Kuala Lumpur some time prior to their being handed
over to Indonesia authorities in March 2008. Husna and Purwantoro apparently made
their way from Indonesia to Malaysia undetected and had reportedly been given fake
passports and plane tickets for Syria by an Algerian known as Jafar. The pair
reportedly met with Jafar in both Kuala Lumpur and Jakarta. Their Syrian destination
and contact with Jafar has led to speculation that the two were headed for Iraq and
that JI has maintained contact and linkages with outside terrorist groups despite its
having been severely disrupted. Sydney Jones with the International Crisis Group has
reportedly stated “It suggests an international network with a base in Jakarta and
raises all sorts of questions about who else might be here.” It was also reported that
the two had received bomb making training at JI training camps in the southern
Philippines in 1999. Purwantoro is thought to have been a leader of JI operations in
Sulawesi.91 There are claims that terrorist group active in southern Thailand have
been able to move across the Thai-Malay border with relative impunity.92

88 “Economic Downturn May Push Up Crime, Says Syed Hamid,” The Malaysian Insider,
June 17, 2008.
89 The D8 is a group of eight Muslim developing nations comprised of Bangladesh, Egypt,
Indonesia, Iran, Malaysia, Nigeria, Pakistan and Turkey.
90 “‘D8’ Agrees to Boost Food Production as Crisis Looms,” AFP, July 8, 2008.
91 “Indonesian Police Details How JI Forge Int’l Terror Links,” The Philippine Star, June

1, 2008.

92 “Malaysia Risk: Security Risk,” Economist Intelligence Unit, May 19, 2008.

For a period in the late 1990s, Malaysia was the locus of JI and Al Qaeda
activity in Southeast Asia. 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 a statement by one captured Al Qaeda leader, Malaysia
was viewed as an ideal location for transiting and meeting because it allowed visa-
free entry to citizens of most Gulf states, including Saudi Arabia.93 Since 2001,
Malaysian authorities have done much in support of the war against terrorists even
as Malaysia has differed with some aspects of U.S. foreign policy.
A Muslim Voice of Moderation. Prime Minister Abdullah has urged
Muslims around the world to guard against extremism and improve ties with the
West while promoting his nation’s moderate version of Islam known as Islam
Hadhari or “Civilizational Islam.”94 According to former Deputy Secretary of State
Robert Zoellick the United States remained confident in Malaysia’s ability to handle
the threat of terrorism.95 Malaysia’s former Prime Minister Mahathir Mohammed,
a longstanding promoter of non-violent Muslim causes, openly criticized Islamic
terrorists, including Palestinian suicide bombers.
Malaysia is an ethnically-diverse, predominantly Islamic nation with large
Chinese and Indian minorities. From its beginnings, Malaysia has sought to balance
its identity as an Islamic nation with its culturally diverse population. Prime Minister
Abdullah has stated that “we are responsible for ensuring that the culture of
extremism and violent acts in the name of Islam does not happen in Malaysia.”96 The
Malaysian government has tried to place itself at the center of the debate within the
Islamic community at fora such as the Organization of the Islamic Conference (OIC)
on what Malaysia sees at the true values of Islam and Islam’s history of religious and
cultural tolerance.
The Malaysian government has been highly critical of U.S. conduct of the global
war on terrorism and its overall Middle East Policy. Malaysia views the U.S.
“invasions” of Afghanistan and Iraq, as well as the continuing “occupation” of Iraq,
as contributing to the growth of membership and popular support of terrorist groups.
In addition, the Malaysian government sees the “pro-Israel” bias of the United States
as a barrier to the resolution of the Palestinian problem and another source of rising
support for terrorist groups. Also, Malaysia has been critical of the perceived U.S.
tendency to “stereotype” terrorism as being a problem peculiar to Islam, contributing
to a rise in anti-Islam rhetoric.97 During the June 2008 gathering of the Organization

93 The 9/11 Commission Report, p. 158.
94 “Malaysia PM Abdullah Warns Muslims Against Extremism,” Voice of America, January

27, 2005.

95 “Malaysia’s Efforts Against Terrorism,” Bernama, June 8, 2005.
96 “Malaysian Premier calls on Muslims to Defy Militants,” Agence France Presse, July 20,


97 Mohd Nasir Yusoff, “M’sia Wants Stereotyping of Terrorism with Islam to Stop,”

of the Islamic Conference, Prime Minister Abdullah reportedly stated, “This biased
view (of Islam) in the West persists, and, I must admit, it is not helped by the
misguided actions of a discredited few from the Muslim side.”98
Maritime Concerns. The threat of seaborne terrorism in the region,
particularly in the vital Straits of Malacca between Malaysia, Singapore, and
Indonesia, continues to be a cause for concern. This is due to the strategic importance
of the sea lanes to international trade and its vulnerability to attacks against shipping.
Malaysia, Singapore, Thailand and Indonesia have made progress in addressing
potential terrorist and pirate threats to maritime shipping lanes in the Straits of
Malacca 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.99 In
August 2007, the navies of Malaysia, Brunei, the Philippines, Singapore and
Thailand participated in a Southeast Asia Cooperation Against Terrorism (SEACAT)
exercise with the U.S. Navy in the Straits of Malacca that sought to provide training
in the area of maritime interception.100 According to the press, the Pentagon recently
awarded a total of $27 million in coastal surveillance equipment to Indonesia,
Malaysia, and the Philippines to “disrupt terrorists plying the Sulawesi sea lanes.”101
U.S.-Malaysia Counter-Terrorism Cooperation
The United States and Malaysia signed a Memorandum of Understanding
(MOU) on counter-terrorism in May 2002. The text of that document became the
basis for a subsequent declaration on counterterrorism that the United States and
ASEAN signed at the August 2002 ASEAN Regional Forum (ARF) meeting.102
Shortly after taking office in the fall of 2003, Prime Minister Abdullah pledged103
to continue Malaysian support for the war against terror. As previously discussed
in this report, Malaysia has repeatedly attempted to play the role of facilitator of talks
between the governments and indigenous separatist groups in Southeast Asia,
including taking the role as chief facilitator of talks between the Philippine
government and Moro Islamic Liberation Front (MILF). However, in a statement

97 (...continued)
Bernama, March 5, 2007.
98 “Muslim Leaders Urge Western Governments to Condemn Acts that Insult Islam,”
Associated Press, June 9, 2008.
99 Michael Richardson, “Maintaining Security in Malacca Strait,” The Jakarta Post, January

11, 2006.

100 “Malaysia, Singapore Boardings Wrap Up Anti-Terrorism Exercise,” US Fed News,
August 21, 2007.
101 Eric Schmitt, “Experts See Gains Against Asian Terror Networks,” New York Times, June

9, 2008.

102 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 ].
103 “Malaysia Pledges Terror Fight,” The Wall Street Journal, November 4, 2004.

before the Organization of Islamic Conference (OIC) Prime Minister Abdullah
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.104
During his July 2004 meeting with President Bush in Washington, DC, Prime
Minister Abdullah sought to strengthen bilateral ties with the United States.105
Following his visit, Abdullah urged that the war on terrorism take into account the
root causes of terror and warned that if it does not “for every one we kill, five more
will emerge to continue their struggle.”106
The extent to which the United States depends on “Malaysia to be an effective
and cooperative player in the region’s vital counterterrorism programs” was
highlighted by James Keith in testimony before the Senate Committee on Foreign
Relations in May of 2007. Keith stated that “Prime Minister Abdullah Badawi has
set a path forward that promises an increasingly productive relationship and greater
congruence between the interests of America and Malaysia.”107
Terrorism and Counter-Terrorism in Malaysia
The level of terrorist activity in Malaysia is considered comparatively low. Stiff
new laws and police activity have purportedly undermined the previously existing
networks of terrorism in Malaysia. The Malaysian government has purportedly
sharply reduced the activities of the JI and Al Qaeda. Other groups reportedly active
in Malaysia include the Abu Sayyaf Group and the Kampulan Mujiheddin Malaysia
The Abu Sayyaf Group once engaged in several terrorist actions in Malaysia. In

2000, a Philippine-based Abu Sayyaf cell abducted tourists at two Malaysian resorts,

returned to the Philippines, and held them hostage for a period of time. The hostages
from Malaysia were eventually freed or rescued, but some hostages from other
attacks were killed by Abu Sayyaf. The group reportedly split from the much larger
Moro National Liberation Front in the early 1990s under the leadership of Abdurajak
Abubakar Janjalani.
The KMM is a small, militant group calling for the overthrow of the Malaysian
government and the creation of a pan-Islamic state encompassing Indonesia,
Malaysia, 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.

104 “Time For US to Change its Image,” Today, January 28, 2005.
105 See CRS Report RL33878, U.S.-Malaysia Relations:Implications of the 2008 Elections,
by Michael F. Martin.
106 “Disquiet as Bush Dominates Agernda at Asia Pacific Sumit,” Agence France Presse,
November 21, 2004.
107 James Keith, Ambassador Designate to Malaysia, “Nominee to be Ambassador to
Malaysia,” U.S. Department of State, May 22, 2007.

In June 2008, Malaysia’s Home Ministry began investigations into a claim that
Malaysians were involved in a plot with members of the Liberation Tigers of Tamil
Ellam (LTTE) to plant a bomb in Colombo, Sri Lanka.108 Home Minister Hamid has
reportedly stated, “If it is true that some Malaysians are involved with the LTTE, we
will take severe action.” Also in June 2008, the Malaysian government began
withdrawing its peacekeepers in the southern Philippines, supposedly as a sign of its
impatience with the progress of talks between the Moro Islamic Liberation Front
(MILF) and the Philippine government.109
Malaysia has passed a number of laws as part of its counter-terrorism efforts.
The most prominent and criticized law is the Internal Security Act (ISA). Originally
passed in 1960s during a national state of emergency, the ISA allows for the arrest
and detention of people without charge for up to two years if the Home Minister
determines that the detainees pose a threat to national security. Other counter-
terrorism laws went into effect in March 2007 that provide for the forfeiture of
terrorist-related assets, allow for the prosecution of those who materially support
terrorists, and expanded surveillance of suspects.110
There have been repeated allegations that the Malaysian government has used
and continues to use the ISA and other counter-terrorism laws to suppress political
opposition. In November 2007, several members of Malaysia’s Hindu Rights Action
Force (HINDRAF) were arrested following a demonstration to protest the destruction
of Hindu temples. Most of HINDRAF members arrested were subsequently released.
However, on December 12, 2007, Prime Minister Abdullah signed two-year
detention orders for five of the detained HINDRAF leaders under the provisions of
the ISA, claiming that the organization has ties to international terrorist groups, such
as the LTTE. HINDRAF has reportedly denied it has any links to the LTTE or other
terrorist groups.111 In addition to the so-called “HINDRAF Five,” there are reportedly

70 other ISA detainees in Malaysia, including purported JI members.

There is opposition to the ISA and other counter-terrorism laws in Malaysia in
part of their abuse for political purposed, and in part because of their infringement
of civil liberties. In June 2008, the Malaysian Bar Council called on the Malaysian
government to abolish the ISA following a court decision awarding $800,000 in
damages to a political activist who was arrested and detained. The court ruled the
activist’s arrest and detention was clearly done for political reasons, and were not
based on any threat to national security.112

108 “Probe on Malaysian Link to Colombo Bomb Attack Plan,” The Malaysian Insider, June

17, 2008.

109 “Philippines Seeks More Peacekeepers to Replace Malaysians,” The Malaysian Insider,
June 4, 2008.
110 For more information, see U.S. Department of State, Country Reports on Terrorism,
release on April 30, 2008.
111 “Those Linked to Terror Groups to Face Consequences,” The Star, December 9, 2007.
112 “Move to Abolish Malaysian Security Law Gathers Strength,” IANS, June 20, 2008.

Shortly after the September 11, 2001 attacks in the United States, Singaporean113
authorities launched aggressive operations to counter terrorist activities. Under
its Internal Security Act, Singapore has arrested dozens of suspected Islamic
militants, 34 of whom remain in detention. Many of the militants are alleged to be
members or sympathizers of JI. In 2002, Singaporean authorities reportedly
uncovered a JI plot to bomb the U.S. Embassy and other western targets in
Singapore. Authorities claim that many of the suspects have links to the Philippines-
based Moro Islamic Liberation Front (MILF).
Despite its strong counter-terrorism record, Singapore was embarrassed by the
February 2008 high-profile prison escape of Mas Selamat bin Kastari, the alleged
head of JI in Singapore. Mas Selamat was accused of plotting the embassy bombing.
A government report issued two months after the escape, with the prisoner still at
large, concluded that there had been no inside cooperation in Mas Selamat’s escape
from the tightly-guarded Whitley Detention Center.
U.S.- Singapore Cooperation
The Joint Counter Terrorism Center (JCTC) coordinates the multiple agencies
and departments of the Singaporean government that deal with terrorism, including
the intelligence agencies. 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 JI 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 neighboring countries. Singaporean
authorities have shared information gathered from suspected militants held under the
Internal Security Act with U.S. officials, reportedly providing detailed insights into
JI and Al Qaeda’s structure, methods, and recruiting strategies.
Singapore was a founding member of the Proliferation Security Initiative (PSI),
a program that aims to interdict shipments of weapons of mass destruction-related
materials, and 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 to pre-screen U.S.-bound containers. Singapore has led other littoral
states in Southeast Asia to jointly protect the critical shipping lanes of the Straits of
Malacca from piracy or terrorist attacks.
Enhanced Homeland Security
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

113 For more information on Singapore, see CRS Report RS20490, Singapore: Background
and U.S. Relations, by Emma Chanlett-Avery.

armed personnel at a major petrochemical hub. Singapore has revamped its national
security bureaucracy and instituted a “Total Defense” campaign, which calls on all
Singaporeans to participate in the national defense. The government intends to
psychologically prepare its public for an attack by framing the question of a terrorist
attack as “when, not if.” A large-scale anti-terrorism exercise in June 2005 involved
over 1,000 citizens and public officials and Singapore’s public transit systems. The
regulation of people and goods across Singapore’s borders has been intensified
through the merging of the border control functions of the customs and immigration
services. To strengthen border security, Singapore has introduced a biometric
passport holding a chip that provides the owner’s facial and fingerprint identification
information. Singapore instituted a Strategic Goods Control (SGC) system that aims
to prevent the proliferation of weapons of mass destruction, and is active in
international fora that focus on export control regimes, including the Export Control
and Related Border Security Assurance (EXBS) program organized by the U.S.
Department of State.
Options and Implications for U.S. Policy
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 Thailand.
To date the U.S. approach to fighting terrorism in Southeast Asia primarily has
been bilateral rather than multilateral in nature. 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 ideologies.
Thus far, the strategy of arresting Jemaah Islamiyah’s leadership is thought to
have crippled JI’s capabilities significantly. This may mean that a continued push
to arrest the network’s leadership could dramatically reduce JI’s ability to threaten
Western targets directly. Additionally, it appears that middle and lower-level JI114
functionaries’ level of commitment may not be as fanatical as commonly thought.
However, the apparent ability of JI to remain operational despite the elimination
of most of its leadership indicates that a decapitation strategy alone is insufficient.115

114 Rohan Guanaratna, “Al-Qaeda’s Operational Ties with Allied Groups,” Jane’s
Intelligence Review, February 1, 2003.
115 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

Attacking camps operated by JI and/or the MILF in Mindanao is seen by some as
particularly attractive, as Mindanao may be performing a crucial role as a regrouping
and training area for JI operatives. Such a course of action would need to be
coordinated closely with regional governments to ensure a common front and prevent
antagonizing local governments and populations through unilateral U.S. action.
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 of alienation among Muslim citizens.116 Options include:
!Placing priority on discovering and destroying terrorist training
centers, which have proven extremely important to JI and the MILF,
in particular;117
!Strengthening the capacities of local governments’ 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 ground
for JI and other terrorist groups to recruit and raise funds;118
!Continuing and expanding support for state-run schools, so that
Muslims are less likely to send their children to radical madrassas
where extremist brands of Islam are propagated;
!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 that encourage economic development;
!Increasing regional cooperation on a multilateral and bilateral basis
with key institutions involved with the war against terror;
!Providing additional 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

115 (...continued)
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.
116 Abuza, “Funding Terrorism in Southeast Asia,” p. 10-11.
117 Jones, “Indonesia Backgrounder,” p. ii.
118 Sidney Jones, “Terrorism In Southeast Asia, More Than Just JI,” Asian Wall Street
Journal, July 29, 2004.

!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;
!Continuing to track terrorism financing. Notwithstanding increased
police cooperation, most Southeast Asian countries do not appear to
have made commensurate efforts to locate, freeze, and at a minimum
disrupt the flow of the assets of Islamic terrorist groups.
!Increase U.S. Pacific Command’s use of international conferences
and exercises aimed at combating terrorism and piracy.119
Other Policy Implications
There is a perception among some Southeast Asians that the United States has
relied too heavily on “hard” 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, political, and ultimately
ideological challenges.”120
Some analysts believe Southeast Asian states perceive the United States as
focused on the war against militant Islamists to the exclusion, or significant
undervaluation, of other issues of more concern to regional states. Added to this are
regional perceptions of an overly militaristic U.S. response in Southeast Asia. There
are others still that see the American war on terror as a war against Islam. Together
these factors indicate a potential disconnect between the United States and regional
states. Such a division has the potential to limit the degree to which regional states
will cooperate with the United States. From one perspective, “Washington stands to
lose ground against Beijing’s diplomatic drive to court regional countries on other,
equally important economic and strategic issues if it remains narrowly focused on
counter-terrorism cooperation alone.”121 A policy approach that focuses more
attention on the region and does more to take into account the concerns of regional
states could, in this view, potentially achieve more cooperation in areas of concern
to the United States including counterterrorism cooperation.

119 United States Pacific Command Joint Interagency Coordination Group for Combating
Terrorism, “Strategy for Regional Maritime Security Initiative,” Version 1.0, November,


120 See Seng Tan and Kumar Ramakrishna, “Interstate and Intrastate Dynamics in Southeast
Asia’s War on Terror,” SAIS Review, Spring, 2004.
121 Amitav Acharya and Arabinida Acharya, “The Myth of the Second Front: Localizing the
‘War on Terror’ in Southeast Asia,” The Washington Quarterly, Autumn, 2007.

Figure 1. Southeast Asia


Figure 2. Indonesia


Figure 3. Malaysia and Singapore


Figure 4. The Philippines

Figure 5. Thailand