Inmates began rampaging through the jail in Medan city on Sumatra island on yesterday afternoon, setting alight fires and hurling bottles at guards in anger over power cuts and water shortages at the facility.
The Tanjung Gusta jail was engulfed in towering flames and scores of firefighters battled through the night to douse them.
Some 150 prisoners, including militants, escaped and police and soldiers were on Friday still desperately hunting for around 100 convicts after recapturing several dozen overnight.
The Justice and Human Rights minister Amir Syamsuddin has held talks with representatives of the prisoners, Akbar said, without giving further details, adding that the minister will hold a press conference later today.
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Prisoners are often held in grim, overcrowded jails in Indonesia, and Tanjung Gusta is no exception as it currently holds well over double its official capacity of 1,054.
The prisoners were seen casually chatting outside their cells early Friday while heavily armed security forces formed a cordon round the building, an AFP reporter at the scene said.
"We don't like police, they are inhumane, they frequently beat us," one of the prisoners shouted, as another waved a charred gun and handcuffs at officers.
Five people -- three prisoners and two prison staff -- had died in the riots, the deputy minister of Justice and Human Rights Denny Indrayana said. The two prison staff had become trapped in their burning office, he added.
About 1,000 police and soldiers were deployed to guard the facility and undertake a massive search around the area Friday to try to find prisoners still on the loose.
Some were jailed for their involvement at a camp in Aceh province where, police say, militants were planning Mumbai-style gun attacks on high-profile Indonesians.