At least 442 inmates broke through a prison gate, overwhelming guards as some tried to set fire to buildings inside the prison.
Police said 242 men had been recaptured by Sunday morning, leaving about 200 still at large.
Inmates in the Sialang Bungkuk Prison had complained about the way they were treated in the jail and also accused some of the guards of violence towards them.
The incident took place at the Sialang Bungkuk prison located in Pekanbaru, Riau province as inmates were allowed out of their cells to take part in prayers in the Muslim-majority country, officials said.
Authorities were initially uncertain about how many prisoners had escaped from the prison, estimating the numbers at between 100 and 300.
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"The prison, which has a capacity of 361, was holding more than 1,870 people", Tejo said.
Three days after the mass escape, 151 prisoners were still on the run and 197 have been recaptured, Ferdinand Siagian, the head of Riau Province's Law Ministry office, which oversees Pekanbaru prison, told Reuters.
More than a thousand inmates who did not escape the prison were refusing to return to their cells unless the head guard was replaced.
As of Monday provincial police chief said the authorities have recaptured 296 of the escaped inmates.
Jailbreaks are common in Indonesia where overcrowding has become a significant problem in prisons that are struggling to cope with poor funding and an influx of people arrested under a war on drugs.
There was a spate of breakouts in 2013, including one where about 150 prisoners - including terror convicts - escaped from a jail on western Sumatra island.