There was an unconfirmed report that five people, including two wardens, were killed.
The Jakarta Globe said police estimated at least 200 prisoners escaped from the Tanjung Gusta Penitentiary in Medan in North Sumatra Thursday night after setting some its offices on fire and storming the main gate and about 55 had been recaptured.
A police chief of detectives identified only as Sutarman said authorities were still trying to determine the exact number of prisoners who broke out.
The Globe report said the inmates had knocked down a prison wall to stage their escape.
Sutarman said police personnel from North Sumatra, West Sumatra, Aceh and Jambi were searching for the prisoners.
The newspaper quoted a police source as saying that five people, including two wardens, were found dead at the prison following the incident but Sutarman said the National Police had not received any reports about the deaths.
"The information is still unclear, and I cannot confirm anything at the moment," he said.
Power outages and water shortage were believed to have triggered the riot, the report said.