THE PAPER | Indonesia’s New Counter-Terrorism Challenges | The Jamestown Foundation

Following the 2002 Bali bombings, Indonesia confronted a seemingly unmanageable terrorist problem. Over the next decade, however, the country became widely viewed as a counter-terrorism success story as the threat from al-Qaeda-linked or -inspired jihadist groups declined dramatically. Unfortunately, the transnational pull of the conflicts in Syria and Iraq, and the emergence of the Islamic State, risk undermining Indonesia’s counter-terrorism successes.

Following the 2002 Bali bombings, Indonesia confronted a seemingly unmanageable terrorist problem. Over the next decade, however, the country became widely viewed as a counter-terrorism success story as the threat from al-Qaeda-linked or -inspired jihadist groups declined dramatically. Unfortunately, the transnational pull of the conflicts in Syria and Iraq, and the emergence of the Islamic State, risk undermining Indonesia’s counter-terrorism successes.

THE PAPER | Indonesia’s New Counter-Terrorism Challenges | Jamestown Foundation

Image Attribute: Detachment 88, Counter Terrorism Unit performing drill, / Source: Wikimedia Commons


In the early 2000s, a range of jihadist groups operated across the Indonesian archipelago. These were not initially considered a major security concern by the government, as Indonesia prioritized rebuilding its economy after the Asian Financial Crisis and consolidating its democracy after overcoming a 32-year-long dictatorship. Additionally, most of these groups confined their violence to the islands of Maluku and Sulawesi, where communal conflicts had broken out between Muslims and Christians.

One such group, Jemaah Islamiyah (JI), had a close relationship with al-Qaeda, dating back to the 1980s foreign fighter mobilization against the Soviets in Afghanistan. JI’s co-founders Abdullah Sungkar and Abu Bakar Bashir were hesitant to follow Osama bin Laden’s 1998 call for attacks on Western military and civilian targets, but one faction of JI chose to join al-Qaeda’s global war. This faction was led by Riduan Isamuddin, a.k.a. Hambali, who had a close operational relationship with 9/11 architect Khalid Sheikh Mohammed. Hambali’s JI faction bombed churches across Indonesia, unsuccessfully attempted to attack the U.S. Embassy in Singapore and in October 2002, bombed tourist venues in Bali, killing 202 people. [1]

In response, Indonesia launched a police-led counter-terrorism campaign, assisted by Australia, the United States and other countries, arresting hundreds of suspected militants. Hambali himself was arrested in Thailand, suspected of planning an attack against the Asia Pacific Economic Cooperation (APEC) summit in Bangkok (The Age, August 15, 2003). One of the Bali bombers, Noordin Mohammad Top, stepped in to Hambali’s role and continued attacking Western-associated targets in Indonesia. His faction bombed the Jakarta Marriot Hotel in September 2003, the Australian Embassy in September 2004 and Bali tourist venues again in October 2005 (Kompas, August 9, 2003).

Each bombing led to further arrests by Detachment 88, a new counter-terrorism unit within the Indonesian National Police. In response to the crackdown, JI’s leadership distanced itself from Noordin’s breakaway faction and eschewed mass-casualty attacks on foreign targets. Instead, they sought a secure base in Poso, a Sulawesi town recovering from recent communal conflict. JI’s Poso network focused on killing Christians and government officials, and in 2005, shocked the nation by beheading three Christian schoolgirls (Jakarta Post, April 26, 2013). In 2007, Detachment 88 killed and arrested many members of the network, prompting JI to cease violence and focus on gradually rebuilding itself.

JI was further weakened in 2008, when their former leader Abu Bakar Bashir created a new organization, Jemaah Ansharut Tauhid (JAT), taking many JI members with him. [2] Noordin’s network, also weakened by counter-terrorism efforts, failed to launch another major attack until July 2009, when it bombed Jakarta’s Marriot and Ritz-Carlton hotels. Detachment 88 killed Noordin in raids after the attack, and his network did not recover (Jakarta Post, August 8, 2009).

Following these setbacks, Indonesian jihadism took a different direction. Leading figures, including clerics and fighters, rejected both the Noordin network’s strategy of prioritizing foreign targets and JI’s approach of favoring outreach over action. Instead they established a training camp in Aceh province, which had experienced decades of separatist conflict. The camp involved every major Indonesian jihadist group except for JI, and received funding from Abu Bakar Bashir’s JAT. Their plan was to hold territory and gradually build up an insurgency, which they saw as the approach taken in the southern Philippines, southern Thailand and Chechnya. [3]

They miscalculated. The aspiring insurgents lacked popular support, and locals soon tipped off the police. In early 2010, Detachment 88 launched raids, killing eight of the militants and arresting 48 others in the following months. [4] Aman Abdurrahman, the camp’s leading spiritual authority, was jailed. Bashir was later jailed for providing funding (Kompas, June 19, 2011).
Indonesian jihadism, thereafter, only continued at a low level. Fragmented networks of jihadists turned to small-scale attacks, robbing stores and killing police officers. Attempted attacks on foreign targets became rare, except for a possible plot against tourists in Bali in 2012 and a failed attempt to bomb the Myanmar Embassy in 2013 (Jakarta Globe, March 22, 2012; Jakarta Post, January 22, 2014). Counter-terrorism efforts had suppressed the most violent networks, but pools of supporters remained and waited for opportunities, which were soon provided by the conflict in Syria.

Indonesian Jihadists in Syria and Iraq

From 2012, Indonesia’s radical Islamist organizations watched the Syrian war closely. Abu Bakar Bashir described the conflict as a “university for jihad education,” and Indonesians joined a range of groups, including the Islamic State (then the Islamic State of Iraq and Syria—ISIS) and al-Qaeda affiliate Jabhat al-Nusra. [5] Their first “martyr” was announced in November 2013, by a Syrian Islamist militia, the Suqour al-Izz Brigade. They claimed Riza Fardi, an Indonesian who had been studying in Yemen and then joined the Syrian uprising, had died fighting in eastern Ghouta (Inside Indonesia, August 3).

By 2014, the Islamic State had become the most popular group for Indonesian jihadists, who began to appear in its propaganda (Tempo, January 5). The al-Hayat Center, an Islamic State media outlet, released an eight-minute Bahasa Indonesian-language video on July 23, 2014, called “Join the Ranks” (Tempo, January 4). The video featured a man later identified as Bahrum Syah, who was a follower of Amman Abdurrahman and left Indonesia in March 2014, at the age of 29 (Kompas, August 6, 2014; Kompas, August 8, 2014). Bahrum Syah called upon “the brothers in Indonesia, [to] have patience, be upright upontauhid (monotheism) and put all your effort into using your physical and financial strength to emigrate to the Islamic State, for hijrah (migration) today is obligatory. It is an obligation decreed by Allah the Exalted.” [6]

In September 2014, Indonesian and Malaysian Islamic State fighters announced the existence of a Bahasa-speaking unit called “Katibah Nusantara Lid Daulah Islamiyah,” meaning the Malay Archipelago unit of the Islamic State. [7] The unit has at least 22 members with combat experience, reportedly brought together because their lack of English and Arabic proficiency created a need for their own unit (Kompas, May 26, 2014).

There are competing estimates of how many Indonesians are involved with jihadist groups in Syria and Iraq. One of the most widely-used estimates is that up to 500 have joined the conflict, including fighters, but also their wives and families (The Strategist, July 17). Around 40 have reportedly been killed (The Australian, July 1). Given Indonesia’s Muslim population is an estimated 209 million, 500 people does not represent a dramatically large level of involvement in Syria and Iraq. [8] Despite this, the conflict’s potential to reinvigorate Indonesian jihadism has led to a proactive response by the government.

Developments at Home

Indonesian authorities are greatly concerned about the foreign fighter mobilization and have arrested several suspects. One suspect was Afif Abdul Majid, who had been the head of JAT’s Central Java branch, had helped fund the failed Aceh camp and was placed on the U.S. Treasury Department’s sanctions list for his terrorist involvement (U.S. Department of Treasury, September 18, 2013). He was arrested in August 2014, after returning from Syria. In December 2014, police arrested a group of six people suspected of planning to join the Islamic State, and then arrested a seventh person, thought to have facilitated their attempted travel (Kompas, December 27, 2014). In March 2015, three suspected Syria returnees were arrested (Jakarta Post, March 27). That same month, Turkish police arrested 16 Indonesians suspected of trying to join the Islamic State (Kompas, March 19). Indonesian police then arrested four men for allegedly arranging travel documents (for these 16 suspected Islamic State supporters and 21 others) (Malay Mail, March 23). 12 of the suspects deported from Turkey were subsequently entered into a de-radicalization program (Kompas, March 26).

However, securing convictions has been difficult. Prosecutors could not convict Afif Abdul Majid for his activities in Syria, even though he admitted training with the Islamic State and pledging allegiance to them (Jakarta Post, July 10). The government banned the militant organization in August 2014, but it is not currently clear what the ban means in practice (Tempo, January 5).

Indonesia’s jihadist groups have increasingly taken inspiration from the Islamic State. Aman Abdurrahman, currently imprisoned for his role in the Aceh camp, pledged allegiance in an online oath to Islamic State leader Abu Bakr al-Baghdadi (Jakarta Post, June 14, 2014). However, support to the Islamic State has not been uncontested. Abu Bakar Bashir pledged allegiance to the organization from prison, but the decision split JAT (Kompas, July 14, 2014). Bashir’s own sons and top aides refused to support the Islamic State and were expelled, going on to form a new group, Jemaah Ansharusy Syariah (JAS – Group of Supporters of Shari’a). Meanwhile JI, which has been quietly redeveloping its military capacity, has sided with Jabhat al-Nusra against the Islamic State (Tempo, January 5).

The Islamic State has also gained support from Santoso, the most infamous Indonesian terrorist currently at large. Santoso is a former JI member who became head of JAT’s Central Sulawesi affiliate in 2010 (IPAC[Jakarta], April 15). By late 2012, he formed a coalition of local jihadist groups in Poso, called Mujahidin Indonesia Timur (MIT), that repeatedly ambushed and killed police officers. His network maintains ties to jihadists elsewhere in Indonesia, as well as in Malaysia and the Philippines (Janes Terrorism & Insurgency Centre (JITC), February 7, 2013). Escaping multiple raids and manhunts, Santoso has since become Indonesia’s most wanted jihadist.

Santoso has released videos taunting police, described himself as “the Abu Musab al-Zarqawi of Indonesia,” and was one of the first Indonesian jihadists to pledge allegiance to IS (IPAC [Jakarta], April 15). His group has not been officially recognized by the Islamic State, but it has received support from jihadists abroad. For instance, on September 2014, police arrested four Uyghurs who had entered Indonesia with fake passports and tried to join Santoso’s militia (Jakarta Post, July 13). They were suspected of having been part of a group that attacked a train station in Kunming in southwestern China (Jakarta Post, February 10).

Another concern has been of Islamic State-connected or -inspired bombings within Indonesia. On February 23, 2015, a small chlorine bomb exploded in a mall on the outskirts of Jakarta, but no one was harmed (Kompas, February 26). Police blamed the attack on Syria returnees, although no suspects have been named (Jakarta Globe, July 11). In July, another mall bombing occurred, which the police linked to the Islamic State’s call for attacks during Ramadan (Kompas, July 11). On August 12, 2015, Indonesian police arrested three men who were allegedly planning an attack to coincide with Independence Day celebrations (Kompas, August 14). The planned attack apparently intended to target police as well as several places of worship in Central Java (Kompas, August 14). Police confiscated 21 improvised explosives and Islamic State-related items from the suspects’ homes (Kompas, August 13). The three men reportedly received funding from an Indonesian currently in Syria (Kompas, August 14). As most jihadist attacks in Indonesia since 2010 had been small-scale shootings, these recent plots suggest a potential return to mass-casualty bombings.

Future Prospects

The outlook for Indonesian counter-terrorism is not bleak. The estimated numbers involved in the Syria-Iraq mobilization are relatively small, and many Middle Eastern, North African and Western countries have produced more foreign fighters, both in absolute terms and relative to the size of their Muslim populations. The communal conflicts in Maluku and Sulawesi, in which jihadist groups thrived, ended over a decade ago and show no signs of restarting. Moreover, Indonesia has developed formidable counter-terrorist capabilities over the past decade.

However, while Indonesia’s jihadist networks are not large or widespread, they have proven persistent. Detachment 88 and other counter-terrorism bodies have had tactical successes, but the government has been less successful in its non-coercive effort to undermine support for jihadism. At first, Indonesia’s Countering Violent Extremism (CVE) approach involved ad-hoc initiatives by police, prison authorities and NGOs. However, in 2010, the military was put in charge of CVE, but has so far not proven adept at it (IPAC [Jakarta], June 30, 2014).

Detachment 88’s often-questionable shootings of suspects have also created new grievances for jihadists to use as a rallying cry, potentially undermining CVE attempts (ABC, February 8, 2013). A further issue is increased competition between the military and police. The military plays little substantial role in counter-terrorism, but has recently used the police’s failure to catch Santoso to push for greater involvement; the military also has a receptive ear in the new government of President Joko Widodo (Jokowi) (IPAC [Jakarta], May 25). These factors complicate Indonesia’s counter-terrorism efforts.

The resilience of Indonesia’s jihadist networks meanwhile provides opportunities for the Islamic State. The threat Indonesia faced in the early 2000s resulted in part from local extremist groups becoming involved in the 1980s foreign fighter mobilization to Afghanistan. The current mobilization to Syria and Iraq, if not handled well, could result in a similar escalation of the terrorist threat.

About The Authors:

Andrew Zammit is a Ph.D. candidate at the University of Melbourne and formerly a researcher at Monash University’s Global Terrorism Research Centre

Muhammad Iqbal is a Ph.D. candidate at Monash University, researching violent extremism.

End Notes

1. Solahudin, NII Sampai JI: Salafy Jihadisme di Indonesia (Jakarta: Komunitas Bambu, 2011).
2. “Indonesia: The Dark Side of Jama’ah Ansharut Tauhid (JAT),” International Crisis Group, July 6, 2010,
3. “Indonesia: Jihadi Surprise in Aceh,” International Crisis Group, April 20, 2010,
4. Ibid.
5. “Indonesian Jihadists and Syria: Training Ground,” RSIS, October 14, 2013,
6. “al-Hayat Media Center presents a new video message from The Islamic State: ‘Join the Ranks,’” Jihadology, July 22, 2014,
7. “Katibah Nusantara: Islamic State’s Malay Archipelago Combat Unit,” RSIS, May 26, 2014,
8. “The Future of World Religions: Population Growth Projections, 2010-2050,” Pew Research Centre, April 2, 2015,


Publication Details: 

Terrorism Monitor Volume: 13 Issue: 18, September 4, 2015 - [PDF] by The Jamestown Foundation.

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IndraStra Global: THE PAPER | Indonesia’s New Counter-Terrorism Challenges | The Jamestown Foundation
THE PAPER | Indonesia’s New Counter-Terrorism Challenges | The Jamestown Foundation
Following the 2002 Bali bombings, Indonesia confronted a seemingly unmanageable terrorist problem. Over the next decade, however, the country became widely viewed as a counter-terrorism success story as the threat from al-Qaeda-linked or -inspired jihadist groups declined dramatically. Unfortunately, the transnational pull of the conflicts in Syria and Iraq, and the emergence of the Islamic State, risk undermining Indonesia’s counter-terrorism successes.
IndraStra Global
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