Patrol craft engaged a flotilla of the Liberation Tigers of Tamil Eelam (LTTE) off the coast of Pulmoddai and sank two out of two dozen boats, the official said.
"We believe there were 12 to 16 LTTE cadres in the two boats that were sunk," the official said, adding two navy sailors were wounded in a firefight with the Tiger flotilla.
After a separate ground offensive just south of the Pulmoddai coast at Thiriyai, naval ground troops recovered weapons, pressure mines and a communications set left behind by the guerillas, the defence ministry said.
Security forces suffered no casualties during the operation, but the rebels had shot at nearby fishermen, killing two and wounding one, the ministry said.
There was no immediate word from the Tigers about the pre-dawn sea battle.
The LTTE has waged a 35-year campaign for independence that has claimed more than 60,000 lives.
More than 4,800 people have been killed in the latest upsurge of fighting that began in December 2005.