In the last decade, Indonesia’s strategy to combat terrorism through police action and criminal prosecution, not military means, has successfully curbed the local terrorist threat. However, there is growing concern that the rise of the Islamic State in Syria and Iraq could reignite radical movements in the world's largest Muslim-majority country.
At the al-Hikam boarding school, located outside Jakarta, young Indonesian men are learning to counter radical Islamic ideology with moderate Muslim teachings.
The director of this government-funded program, Arif Zamhari, said the newly trained religious scholars will be sent out to speak in mosques across the country.
"We spread a virus of peaceful Islam to our community here. The problem here is you know the loudest voices are from the radicals, so our moderate groups never speak out," said Zamhari.
The last major terrorist attack in Indonesia, the bombing of two hotels in Jakarta, occurred in 2009. That marked the end of nearly a decade of deadly plots by Jemaah Islamiyah and other Southeast Asian militants affiliated with al Qaida.
The government was able to curb the terrorist threat in Indonesia by capturing, not killing, terrorist leaders like Muslim cleric Abu Bakar Bashir. The trials helped turn public opinion against violent militants.
But the terrorist threat re-emerged this year in an online video featuring a purportedly Indonesian Islamic State fighter in Syria exhorting Muslims to rise up against the government in Jakarta.
Sidney Jones, with the Institute for Policy Analysis of Conflict in Jakarta, said the video was a wake-up call.
"The Indonesians for the first time saw the Islamic State as a challenge to Indonesian sovereignty. That's what triggered the reaction. It wasn't that suddenly it became more dangerous," said Jones.
Police have since arrested some local Islamic State supporters and may prosecute them for aiding rebellion in a friendly foreign state. Authorities may also revoke the passports of the estimated 150 Indonesians who have joined the Islamic State in Syria.
Despite concerns from some human rights groups of heavy-handed police tactics with little civilian oversight, the country is sticking by its counter-terrorism strategy.
Some moderate Islamic leaders support blocking religious education funding from outside groups, especially from Iran and Saudi Arabia, but such a ban would include Christian missionary organizations as well.
Sidney Jones said more Indonesian Muslims are using social media to speak out against the extreme violence practiced by the Islamic State.
“One of the interesting things about the emergence of the Islamic State is how horrified most mainstream Muslims are in Indonesia,” said Jones.
The new threat has reminded many Indonesians that despite nearly five years without a major attack, their own war against terrorism is not over.
Producer Ade Irma in Jakarta contributed to this report.