Police said 242 men had been recaptured by Sunday morning, leaving about 200 still at large.
Authorities were initially uncertain how many prisoners had escaped, estimating the numbers at between 100 and 300.
Police said some of the men surrendered or were returned by their families and others were captured by local residents, police and soldiers.
Various officials have said the prisoners were angry about poor conditions and treatment. The prison has a capacity of about 360 but was holding more than 1,870 men, according to a local police spokesman, Guntur Aryo Tejo.