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.
A riot has injured prisoners and some officers at a police detention center south of Indonesia's capital.
Indonesian police said on Tuesday that some officers and inmates had been hurt after clashes at a high-security jail, but denied reports of fatalities at the facility on the outskirts of the capital Jakarta.
A prisoner had also been killed at the jail in Depok, National police spokesman Muhammad Iqbal told reporters. The prisoners are suspected of having taken weapons from the police who were killed.
Authorities said the riot began when an inmate shouted and banged on the walls to protest a delay in getting food from his family that was being checked by officials.
But a link to Islamist terrorists was made after a publication of the Islamic State group's Amaq News Agency.
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Before that, he served as prime minister, from 2003 to 2014. " Turkey will be even more attractive to investors", Erdogan said. Meanwhile, the military also said that the number of terrorists neutralized in Operation Olive Branch has reached 4,403.
"If they surrender, it will be a non-violent process".
"We have isolated them into one block, so the situation is under control", General Iqbal said. Other inmates broke into the ammunition room and seized long-barreled weapons, leading to a shootout with counterterrorism officers, they said.
Police maintained tight security around the jail on Wednesday and kept onlookers away.
IS sympathizers have carried out a series of low level attacks in Indonesia in recent years.
In January 2016, four Islamic State-linked militants mounted a gun-and-bomb attack at a busy intersection outside a Starbucks cafe in central Jakarta, killing themselves and four others.