The statement came after the defence ministry said three rebels were shot dead by naval troops in the nearby eastern coastal town of Trincomalee on Saturday.
"Three Dvora FACs (fast-attack craft) were damaged in the (sea) clash. Two Sea Tigers were killed in action," the rebel Liberation Tigers of Tamil Eelam (LTTE) said in a statement.
The military however said it had thwarted a sea-based guerrilla attack.
"Over 15 Sea Tiger boats had arrived to confront the Sri Lanka navy," the defence ministry said. "Navy troops confirm that the LTTE had sustained severe casualties.
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In other fighting, security forces said they shot dead a suspected Tamil Tiger rebel in the eastern Batticaloa district as a group of guerrillas fled from the jungle regions of Thoppigala.
The statement did not say if troops suffered casualties.
The latest deaths in the 35-year ethnic conflict came as the military intensified attacks to gain control of the island's east, particularly a jungle area known as T