More than 700 Indonesians are taking part in deradicalisation programmes across the country, counter-terrorism chief Suhardi Alius told Parliament.
They include 242 inmates serving time for terrorism-related offences, and others who are not behind bars but have signed up voluntarily, said the head of the National Counter-terrorism Agency (BNPT).
But many more extremists, including militants who recently returned from Syria or Iraq, continue to live freely in Indonesia.
This is because they cannot be detained under current anti-terrorism laws in the country - even though they are known to have travelled to the Middle East and fought as members of militant groups.
The BNPT estimates that 500 Indonesians have gone but it is hard to put an exact number on how many have returned. However, on Thursday, General Suhardi said his agency has identified 47 such "returnees" so far, and President Joko Widodo has ordered that they be placed under surveillance.
"It is not only BNPT, but also the police and other institutions, such as the regional governments, that are helping us monitor these foreign fighters," said BNPT deputy chief Petrus Reinhard Golose.
The agency did not elaborate further on the watchlist during its presentation to the House on Thursday.
The Straits Times was told by a third counter-terrorism official after the meeting that 30 of the 47 Indonesians had joined the Islamic State in Iraq and Syria (ISIS), while the remaining 17 were with Jabhat al Nusra, an Al-Qaeda-linked group based in northern Syria.
The BNPT official, who asked not to be named for security reasons, also said that not all were combatants. "Some returned because they were disappointed after only being given menial tasks, but there were others who were ordered by ISIS to take the fight back home," he added.
Most of the 47 who have returned from the Middle East since 2014 came from Central and West Java - historical hotbeds for militant activity. For instance, extremist ideologue Aman Abdurrahman and the four men who mounted the Jan 14 attack in Jakarta were based in West Java. Bahrun Naim, now in Syria fighting for ISIS and also linked to the plot to fire a rocket at Marina Bay from Batam, used to live in Central Java, as did firebrand cleric Abu Bakar Bashir.
Islamic extremism, however, has a nationwide reach said Gen Suhardi, who said that the 478 Indonesians undergoing deradicalisation outside of prisons come from 17 provinces across the country. These include 107 family members of terrorists, including women and children.
The BNPT is also trying to locate about 200 more local militants, including former inmates, who may not be high-priority targets now but still pose a security risk.
Hundreds of Indonesians have travelled to the Middle East to support or fight for ISIS since 2013. But many have been deported, mainly from Turkey, after being caught trying to cross the border into Syria.
Dr Petrus said there are 302 such deportees who did not manage to link up with other militants.
Separately, The Jakarta Post reported on Thursday that East Indonesia Mujahideen (MIT) leader Basri was with his wife Nurmi Usman, alias Oma, when he was captured on Wednesday.
The MIT was once headed by Indonesia's most wanted terrorist Santoso, the main target of troops deployed for Operation Tinombala. Their mission was to kill or capture Santoso and members of the group.
Basri and his wife did not resist when they were ambushed by security forces in Poso, Central Sulawesi, but another militant, named Sobron, managed to escape, said Tinombala spokesman Hari Suprapto.
Troops also found the body of MIT fighter Andika Eka Putra along a river on that same day.
Previous reports had said Andika was shot dead, but General Hari said he may have died from a fall. "But we will verify (that) after we interrogate Basri," he added.