Five sailors were killed in the attack, the military said.
The rebel Liberation Tigers of Tamil Eelam (LTTE) were believed to have lost at least six fighters after firing on two naval craft off the northwestern Kalipinya lagoon, it said.
"We destroyed two Tiger boats and they had at least three people on board each boat.
We believe they were killed," navy spokesman P.D.K. Dassanayake said.
One navy boat was sunk and three sailors were also wounded, according to the defence ministry.
The Tigers also killed a soldier and wounded six other people, including three civilians, in two mortar attacks early Wednesday in the northeastern district of Trincomalee, defence ministry spokesman Prasad Samarasinghe said.
There have been sporadic attacks on military bases in the embattled northeast as a 2002 ceasefire between the government and LTTE appears on the verge of unravelling.
At least 825 people have been killed in an upsurge of violence since December.
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Amid the deteriorating securi