The rebels said they had recovered the bodies of 13 government soldiers and had taken another prisoner, but the defence ministry said only two soldiers were killed while a search operation was under way for the missing dozen.
Security forces said they had found the bodies of 12 Tamil Tiger rebels and estimated that 40 to 45 rebels were killed in the fighting.
The rebels said only five of their fighters were killed.
The defence ministry also said that 23 soldiers were wounded during fighting in Batticaloa district.
However, a hospital in the adjoining district of Polonnaruwa said 55 government troopers were brought there for treatment.
Both the government and the Tigers have accused each other of triggering the latest fighting which is seen by diplomats as a major setback to reviving