But experts said that the authorities had been reluctant to rein in clerics and schools that had allowed extremists like Noordin to continue operating.
“On the law enforcement side, the achievements have been certifiable,” said Sidney Jones, an expert on Islamic terrorism at the International Crisis Group’s branch in Jakarta.
But Jones said there were an estimated 50 schools with ties to Jemaah Islamiyah where fugitives were sheltered, new recruits were found and money was raised.
“These places remain nodes of communication that are critical to keeping the network alive,” she said. “Everybody knows where these schools are, but there’s been a sensitivity in dealing with them because people don’t want to see Islamic education stigmatized.”
Islamic schools, called pesantren in Indonesia, have long played a central role in many Indonesian communities. Only a few are said to espouse violent tactics. But the schools, which are politically powerful, have long resisted greater government scrutiny.
“It would be very difficult to start questioning ulamas from these schools,” said a senior Indonesian counter-terrorism official, referring to Islamic scholars at the schools and speaking on the condition of anonymity because he was not allowed to speak to the media. “Even moderate Indonesians would react negatively against that.”
The official said that sensitivity about carrying out any measure with a tinge of the pre-democratic Suharto era also complicated investigators’ activities. While permits were needed to publish books in the past, publishers of radical ideology are now flourishing in Indonesia and account for the biggest source of such thought in Southeast Asia.
“Since democratization, we’ve been in a conundrum,” the official said. “Do we start banning books? We’re conscious that we have not eradicated the deeper problems in the last five years.”
Gunaratna, of Nanyang Technological University, said Indonesia needed to adopt tougher anti-terrorism laws, like those in Singapore and Malaysia, which allow suspects to be detained and questioned longer without bringing charges.
“That’s the reason there has been no attack inside Singapore or Malaysia,” he said. “Since democratization, some members of the Indonesian elite have the misguided view that these measures are anti-democratic.”
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