In November 2020, a riot erupted at the facility in which 11 inmates were shot and killed, and nearly 120 others wounded.
The latest unrest came almost a month after another prison riot in the same region, in which 10 guards and 21 inmates were killed.
Medawatte said inmates at Mahara Prison had completely destroyed the kitchen, the hospital, a newly built rehabilitation building and vocational training facilities.
The prison housed 4,100 inmates, about four times its capacity, an issue common across the country's jails.
Last month, the authorities announced plans to convert disused state buildings into prisons.
More than three-quarters of the inmates in Sri Lanka are remand prisoners awaiting trial, and most are held in connection with drug offenses.