It accused the Tigers of killing three civilians and seriously injuring another as a group of people tried to flee rebel areas in six boats.
The ministry did not give its own casualties, but said troops recovered weapons from the Tigers who were killed on Friday.
There was no statement from the Tiger rebels, who have been cornered in a narrow strip of land in Mullaittivu.
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The military has said it hopes to defeat the Tigers completely by April, bringing an end to decades of armed conflict.
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The Tigers, who have been fighting since 1972 to carve out a separate Tamil homeland in the majority Sinhalese island nation, have lost much of their territory in the past two years.