Minister Chandrasiri Gajadeera told parliament that 27 people were killed in Friday's rioting at Colombo's maximum security Welikada prison where inmates fought gunbattles with elite police commandos who carried out a search.
"Sixteen bodies are at the hospital and another 11 were found in the prison today," Mr Gajadeera said in a special statement to the legislature. "I have appointed a three-member committee to investigate the incident."
Army spokesman Brigadier Ruwan Wanigasooriya earlier said troops recovered six bodies of inmates from the prison on Saturday morning.
"During our search operation this morning, we found six dead bodies of inmates in addition to the 16 bodies at the hospital last night," Mr Wanigasooriya told AFP.
He said prison guards and police had also carried out searches and may have recovered more bodies.
The minister said rioting inmates had seized 82 guns, including automatic assault rifles, from a prison armoury they broke into, but the authorities were able to recover most of them.
"A search is on for five weapons which are still missing," the minister said.
Hospital sources said that at least one prison guard was among those killed. Thirteen police commandos and four soldiers were also among 43 people who were wounded in the riot.