"We first fired a warning shot, but the boat did not stop," Dassanayake said. "Thereafter, the boat was blown out of the water.
We don't know about casualties."
Earlier this week, the rebel Liberation Tigers of Tamil Eelam (LTTE) sank a navy patrol craft off the island's northwestern coast, killing five sailors.
In the northeastern port district of Trincomalee, the military fired mortar bombs at suspected Tiger gun positions Saturday, but there were no reports of casualties, a local military official said.
Sporadic attacks against military bases in Sri Lanka's embattled northeast have come 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.
Amid the deteriorating security situatio