Indonesia's National Intelligence Agency (BIN) is tracking at least 100 citizens said to have returned home from the Middle East after joining the Islamic State in Iraq and Syria (ISIS).
Also, funds from the terror group are said to have found their way to militants operating out of provinces such as Central Sulawesi, where Santoso, the country's most wanted terrorist, is believed to be based.
Spy chief Sutiyoso said BIN is monitoring the men who have returned, but stopped short of revealing operational details of the agency's efforts.
The Straits Times understands that the Indonesians were deported from Turkey, which has served as a gateway for hundreds from South-east Asia who aspire to join the ranks of ISIS.
Smugglers have been slipping through the porous border between Turkey and Syria to take foreigners into ISIS territory, where they link up with militants at training camps.
Latest estimates from security agencies in Indonesia, Malaysia, Singapore and the Philippines show at least 900 people from the four countries travelled to join ISIS in Syria.
The largest group, of about 700, were from Indonesia - home to the world's largest Muslim population.
But national police chief Badrodin Haiti yesterday disputed the figures from BIN. He told online news site Tribunnews.com that the number of Indonesians returning after joining ISIS in Syria was "not that high, only around 60 to 70".
Some of them, General Badrodin said, had returned voluntarily, while others had been deported. "We already have all of their complete identities," he added.
All of them, however, were released after being questioned by counter-terrorism police because there are no laws that allow for preventive detention in Indonesia - even though some of them had intended to join ISIS or admitted to having fought with the group in Syria.
Last week, officials said 46 of them - all men of "fighting age" - remained under surveillance by counter-terrorism forces to ensure that they do not propagate ISIS ideology or mount terror attacks at home.
"We will continue to monitor their movement - our personnel in the field will keep watching them," said Gen Badrodin.
An Indonesian Foreign Ministry official, speaking during a dialogue with foreign correspondents in Jakarta on Monday, said figures of "returnees" were confusing as not all of them joined ISIS as fighters.
Unlike Al-Qaeda, which recruits individuals, ISIS also recruits families with children.
"We are in the process of amending our law, with a number of new elements to be included, including how to criminalise those who join military training abroad," said Mr Andy Rachmianto, the ministry's director for international security and disarmament.
A report in The Jakarta Post yesterday said ISIS propaganda is believed to have spread to at least five Indonesian provinces - East Java, Lampung (Sumatra), Central Sulawesi, South Sulawesi and West Sulawesi.
National police spokesman Anton Charliyan was quoted as saying the East Indonesian Mujahidin terrorist group, led by Santoso, had received funds and other assistance from ISIS. "The Santoso group is part of the ISIS network," he added. "You can see that the Poso terror group even has anti-tank weapons."
Poso is located in Central Sulawesi.
Several terror threats issued recently, including a nine-minute video on social media sites that called for strikes on the Jakarta police headquarters and the presidential palace this weekend, were attributed to Santoso. The videos have since been blocked by the authorities.
General Anton said a manhunt is now under way to arrest Santoso and his band of terrorists.