Despite having been nearly wiped out by intense police pressure, Indonesia’s violent extremists are finding ways to regroup, using old networks to build new alliances, according to a new report by the International Crisis Group.

The jihadists were smashed in the wake of bombings in Bali in 2002 which killed 2002 people in the Kuta tourism district and injured 240 in what was called the deadliest act of terrorism in Indonesia’s history. Three of the bombers were executed and a fourth killed in a gunfight with police.

While the police have been relatively effective against the violent Islamists, however, they have been almost criminally negligent in protecting minority members of the society against threats from mainstream Muslim groups. The tendency of the National Police is to look the other way in cases where mobs beset the Ahmadiyah sect, as happened when a Muslim mob descended on sect members in Bogor on July 15, beating them for being in company with western journalists. The police then forced the Ahmadiyah members to apologize for the incident and said no one would be arrested because there were no suspects.

In what seems a particularly toothless statement, the report recommends suggests that the government “must…design and implement a policy of zero tolerance toward any religiously-inspired violence, including maximum sentences for vandalism, assault and threats of violence, with clear instructions to all government employees, including police, to shun interaction with groups or members of groups that have a known history of such activity.”

As to the violent extremists, however, the National Police’s Densus 88 unit has an impressive record of killing or capturing militants, most recently in March when they killed five suspected terrorists after keeping them under surveillance for a month. In 2009, Densus 88 rolled up a long string of terrorists in shootouts in Central Java, killing, among others, Noordin Mohamad Top, perhaps Southeast Asia’s top jihadi terrorist, among others. In the shootout that netted Noordin, three other suspects were killed as well, and a woman in the house was wounded. In early August 2009, police also killed two other suspected militants and found 500 kilograms of explosives in a raid on a house in the Bekasi area near Jakarta.

However, according to the report, the militants are finding ways to regroup on the run, in prison and throughout Internet forums, using social media to remain in communication. The ease with which wanted men can move around, communicate with friends in prison, share information and skills, disseminate ideology, purchase arms, conduct training and recruit new followers shows how much basic preventive work still needs to be done, the report notes.

“In many cases, the same individuals keep reappearing, using old networks to build new alliances,” the report says.” The fact that they have been singularly inept in their operations in recent years does not mean that the danger of attacks is over. There are signs that at least some are learning lessons from past failures and becoming more sophisticated in recruitment and fundraising.”

The police severely crippled militant operations in early 2010 when they raided a training camp in Aceh on the northern end of Sumatra, capturing or killing many senior leaders and discovering information that led to the arrest, trial and imprisonment of 200 individuals.

“Instead of cowing the jihadis into submission, however, police operations inspired a new wave of activity motivated by the desire for revenge, with new partnerships and training centers established and new plans set in motion,” the ISG said. Underground activity directly or indirectly assisted by radical imams has cropped up in Medan, North Sumatra; Poso, Central Sulawesi; Solo, Central Java; Bima, West Nusa Tenggara; and parts of East Kalimantan.

Almost a dozen plots since the 2010 raid have been connected directly or indirectly to the fugitives from Aceh.

Many of the jihadi groups operating today have links to Jamaah Anshorut Tauhid (JAT), a group set up by the radical cleric Abu Bakar Bashir in 2008 that has replaced Jemaah Islamiyah (JI) as the country’s largest and most active jihadi organization. Bashir has repeatedly been jailed for fomenting terrorism only to be freed by the courts. He was most recently convicted in June 2011 and sentenced to 15 years in prison. After a Jakarta High Court reduced the sentence, the Supreme court reinstated it.

Jemaat Islamiyah, which was held responsible for the 2002 Bali attack, continues to exert an influence through its schools, despite disapproval on the part of other militant groups supposedly because of its abandonment of jihad.

Several smaller groups have emerged as well, often composed of inexperienced young amateurs who lack the skills, discipline and strategic vision of the so-called Afghan generation, the jihadis who trained on the Afghanistan-Pakistan border between 1985 and 1994 and produced the Bali bombers, the report notes.

The militants have learned from the Aceh experience, in which a web of jihadi organizations were training together. Today they are more aware of how their ranks have been infiltrated by Indonesian police intelligence, concluding they must be more careful about vetting members and protecting their communications, lessons the previous generation learned in Afghanistan and Pakistan. Most of that generation have been wiped out or neutralized.

“There has been less introspection within the government about why recruitment continues to take place or why there are so many more terrorist plots – even if most have been poorly conceived,” the report notes, pointing out that the police have become skilled at identifying and arresting those responsible for violent crimes and interdicting plots, but there are virtually no effective programs are in place to address the environment in which jihadi ideology continues to flourish.

The report suggests that the Indonesian government adopt 20 recommendations designed to thwart further terrorism. They include designing a study to determine what networks the extremists use to evade police when they believe they are under surveillance, perhaps by further interrogation of the 200 militants they arrested at the Aceh camp.

Other recommendations include designing programs to reduce the influence of radical clerics such as Abu Bakar Bashir, strengthening the analytical capabilities of the National Anti-Terrorism Agency, developing better information-sharing coordination between law enforcement groups and speed up efforts to identify and monitor high-risk detainees, both while in detention as well as after their release.

The government must also close loopholes in airport security that allow passengers to present false identification without fear of detection and to make more systematic use of the expertise of young Indonesian scholars when developing policy on countering extremism.

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