The inmates began rampaging through the jail in Medan city on Sumatra island yesterday afternoon, setting 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 initially escaped and police and soldiers were today still desperately hunting for about 100 after recapturing several dozen overnight.
Prisoners were still in control of the jail early today, casually chatting outside their cells while heavily armed security forces formed a cordon round the building, an AFP reporter at the scene said.
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They allowed in about two dozen soldiers but did not let police enter, the reporter said.
"We don't like police, they are inhumane, they frequently beat us," one of the prisoners shouted.
Heru Prakoso, North Sumatra province police spokesman, said that prisoners and a government official would hold talks later in the day in a bid to break the standoff.
Five people, three prisoners and two prison staff, had been killed in the riots, he added.
About 1,000 police and soldiers were involved in a massive hunt around the area on Friday to try and find the prisoners still on the loose.
They included six terror convicts, said Prakoso. The prison had been holding a total of 11 terror convicts, he said.
They were jailed for involvement in militant training in Aceh province, where separatists fought a long struggle against the central government, and robbing a bank to fund terror activities, he said.
Ten civilian guards were briefly held hostages during the riots on Thursday but were released late in the evening, Prakoso said.