The recent uncovering of plots to destroy Buddhist temples to avenge violence against Rohingya Muslims in Myanmar has also cast a spotlight on Indonesians going to fight in Syria's civil war.
One of the six shot dead in a counter-terrorism raid on New Year's Eve, Nurul Haq, was preparing to travel to Syria to fight alongside militants attempting to topple the government of President Bashar al-Assad, said police.
This discovery lends weight to warnings issued by Indonesia's National Counter Terrorism Agency (BNPT). Its deputy for international cooperation Harry Purwanto has said his agency is tracking 50 Indonesians in Syria for suspected terrorist activities like fighting alongside militants or networking with extremists.
"We view them as threats, and if they come back to Indonesia and carry out any act of violence here, they will be nabbed," he told reporters two weeks ago.
Though the threat of terrorism in Indonesia has been reduced greatly in recent years, analysts warn that terrorists remain resilient and maintain links with old networks to sustain their groups.
The latest revelations show that the conflict in Syria has deeply influenced Indonesian militants, who then travel there and become a threat when they return.
Worse, they could spread sectarian hatred, with the Syrian civil war having become a proxy battle between Sunni and Shi'ite militants, pitting Shi'ites fighting for the Assad regime against the majority Sunni population.
The vast majority of Muslims in Indonesia are moderate, but a radical fringe poses a continuing threat to the mainstream.
Most Muslims here are Sunni, with a small Shi'ite population of three million, who have been harassed by radicals in sometimes deadly clashes. The police have been actively keeping militants in check, but terrorist groups have been waging war against them to avenge killings of their comrades.
Terrorism analyst Noor Huda Ismail noted that the Syrian civil war, now in its third year, has spurred some aspiring terrorists to make the journey there to get training and gather contacts.
"They see Syria as a battleground to carry out their distorted, violent form of jihad," he said. "It is worrying because we don't really know for sure how many have returned... and there is a potential for them to bring back the fight against Shi'ites here."
They are part of over 6,000 foreign fighters believed to have travelled to Syria to assist rebels there since 2011, far higher than the numbers that went to Iraq and Afghanistan to join the wars against the United States-led forces.
Late last year, the Australian government cancelled the passports of 20 men of mostly Lebanese-Australian background for preparing to "engage in politically motivated violence".
Checks on three Indonesian radical websites show that their articles on Syria focus on the Assad government forces' brutality in killing the Sunnis there, and call for Sunni Muslims here to support their counterparts in Syria through donations.
A radical group in Tasikmalaya claimed 100 of its members are ready for battle in Syria, said a report in Jawa Pos News Network last July.
The Institute for Policy Analysis of Conflict noted that the longer the Syrian conflict continues, the greater the chances of more Indonesians getting involved.
Its report last month said that terrorist group Jemaah Islamiah's humanitarian wing, Hilal Ahmar Society of Indonesia, has sent nine missions to Syria for up to a month at a time, and has well-established contacts there.
"All of this is a reminder that the current sense of distance from the global jihad can easily change as more Indonesian fighters go to Syria and return," warned the report entitled Weak, Therefore Violent: The Mujahidin of Western Indonesia.