Sri Lanka's Police Minister, Chandrasiri Gajadeera, told parliament 11 bodies had been found in search operations on Saturday and a further 16 were being kept in hospital.
Heavily armed troops moved into the maximum security Welikada prison overnight on Friday to restore order after hours of gun battle between inmates and police commandos, military officials said on Saturday.
"Police requested our assistance and we deployed troops at the Welikada prison," army spokesman Ruwan Wanigasooriya said.
The overnight toll rose as the injured succumbed to their wounds following intense gun battles between rioting inmates and police Special Task Force (STF) commandos who carried out a search on Friday for drugs and smuggled mobile phones.
Prison authorities said the situation at the jail was now under control and the authorities were in the process of recovering weapons that the inmates had taken from a prison armoury which had been stormed during the riot.
A military officer at the scene on Friday night said inmates had initially grabbed weapons from STF commandos and engaged in deadly gun battles.
During the rioting, some of the convicts had tried to escape and were shot by security forces, witnesses said, adding that tear gas had also been fired at rioting prisoners.
Some of the inmates got onto a roof and fired at troops and police on the ground, while a handful had tried to escape in a hijacked three-wheel taxi.
Police and troops fired back with intermittent gun fire, which witnesses said lasted for at least three hours.
Army troops used armoured personnel carriers to move in reinforcements as inmates kept on firing.
Afghan, Indian and Pakistani inmates were also at the same jail, but none of them had been taken to hospital.
Friday's violence was the worst prison riot since July 1983 when more than 50 ethnic Tamil prisoners were massacred at the same jail by majority Sinhalese prisoners during anti-Tamil riots that had gripped the country.
There was similar violence at the same penitentiary in January when 25 inmates and four guards were wounded.