"Brigadier Iwan Sarjana has been successfully released", National Police spokesman Inspector Gen. Setyo Wasisto said at a press conference as quoted by the Kompas.com news site.
He revealed that a total of 156 terrorist inmates allegedly got involved in the clash, most of whom have surrendered and will soon be transferred to other prisons.
"The majority of terrorism convicts, above 90%, have surrendered", he said.
"We have minimised the number of victims".
The ABC has confirmed five police officers and one inmate have been killed, and another police officer is still a hostage. But after the detention of these terrorists, a set of new threats have emerged recently from Islamic State group.
It is understood that almost all the convicted prisoners involved in the event have surrendered.
The deputy police chief Syafruddin said that during the trouble "five of the officers were killed sadistically".
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Former Jakarta governor Basuki Tjahaja Purnama, an ethnic Chinese Christian who is serving a sentence for blasphemy against Islam at the same prison, was safe and still in the jail, his sister Fifi Lety Indra said.
Islamic State (IS, formerly ISIS) took responsibility for the attack through Amaq, the IS-affiliated website.
A counterterrorism investigator said in a text message that six officers had been taken hostage by the inmates, and five of them were killed.
A dispute had broken out with prisoners who objected to authorities making checks on food being brought into them, according to police.
IS sympathisers have carried out a series of mostly low-level attacks in Indonesia over the past few years. He is on trial for terrorism and is being held at the same prison.
Clashes at the detention center came just one day after the National Police arrested three individuals in Bogor, also in West Java, for supposedly planning a string of attacks on police stations across the province.
In January 2016, four Daesh-linked militants mounted a gun-and-bomb attack at an intersection outside a Starbucks cafe in central Jakarta, killing themselves and four others.