Troops attacked four suspected Liberation Tigers of Tamil Eelam (LTTE) boats off the Jaffna peninsula around midnight Monday, the ministry said.
"These four LTTE boats were destroyed with artillery attacks by the troops," the ministry said in a statement.
It did not say whether there were casualties.
However, the ministry said a suspected Tiger rebel was shot dead on Monday night near the military's defence line in the Jaffna peninsula.
In the northern mainland, a civilian was shot dead Tuesday by unidentified gunmen in Vavuniya, local police said, adding that an investigation was underway.
More than 100 people have been killed in the past three months in Vavuniya, the de facto border town at the entrance to the rebel-held northern Wanni region, official figures showed.
The latest skirmishes came after the navy said it had sunk two cargo vessels believed to be smuggling weapons and explosives for Tigers on Sunday. There was no immediate word from the Tamil Tigers about the s