More than 200 inmates broke out of the jail in Pekanbaru city, on Sumatra island, after they were let out of their cells to pray yesterday.
Almost 80 were quickly recaptured after the incident, and on Saturday the majority had been rounded up.
"So far 209 inmates have been recaptured or surrendered willingly, many have returned to their cells," local police spokesman Guntur Aryo Tejo told AFP, adding that the authorities did not have the exact number of inmates still on the loose.
Most prisoners were recaptured while still near Pekanbaru.
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Dozens of the escaped inmates headed directly to another prison where they handed themselves in.
Tejo said the inmates told the police they decided to escape due to inhumane conditions in the prison.
The male-only prison has a capacity of 300 people but was holding 1,870 inmates, with only five guards and a porter on duty at any one time, said the director general of prisons, I Wayan Dusak.
More than a thousand inmates who did not escape the prison were refusing to return to their cells unless the head guard was replaced.
Jailbreaks are common in Indonesia, where inmates are held in often unsanitary conditions at overcrowded prisons.
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.