Prisons Minister Chandrasiri Gajadeera in a statement said that a three-member probe committee would examine the events which led to the riot.
Over 50 people, including troops were injured in the clash.
The situation was brought under control today after the deployment of the Army's Commando troops, officials said.
Some seven inmates who had fled the jail during the riot have been apprehended, the police said.
A similar search operation in the same prison in 2010 also ended in a riot which seriously injured nearly 50 policemen.