But after the detention of these terrorists, a set of new threats have emerged recently from Islamic State group. But a number of people suffered injuries caused by a riot involving the security forces and the inmates of the terrorism cases in the prison.
Hours before the operation, the police freed an anti-terror squad member who had been taken hostage during the riot after agreeing to comply with the terrorists' demand of food, national police spokesman Brigadier Gen. Setyo Wasisto said.
Iqbal said an inmate was fatally shot after grabbing weapons and threatening officers.
The riot erupted in Depok, on Jakarta's southern outskirts, where four days earlier police arrested three Islamic militants they say planned to attack the headquarters and other police stations in the same town. A counterterrorism investigator said four police officers were wounded and were being treated at a hospital.
The riot began on Tuesday night when the guards refused to give an inmate food brought by his family which led the prisoner to urge other inmates to revolt, according to officials.
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The ABC has confirmed five police officers and one inmate have been killed, and another police officer is still a hostage. "To prevent things from getting worse, we're going to keep negotiating so we don't have to go to the last resort", he added, without elaborating.
IS sympathisers have carried out a series of mostly low-level attacks in Indonesia over the past few years.
The network was neutralized following the arrests of hundreds of its militants and leaders.
A news agency run by Islamic state group published a report stating that prisoners who were detained in the centre were from their group.