Some 40 civilians were also injured in the fighting in Batticaloa, prompted by an attack by some 300 Tiger rebels.
There was no immediate word on the fighting from the Liberation Tigers of Tamil Eelam (LTTE), who have been waging a separatist war since 1972.
According to the defence ministry, the clearing operations have led to the recovery of a large haul of weapons, ammunition and mines left behind by the Tigers after they pulled back to their jungle stronghold of Thoppigala.
Official figures show 148,419 people were listed as internally displaced in the Batticaloa district since the military captured a key base of the Tigers in January.
Since then, the military has also stepped up attacks against Tamil Tiger boats and claimed sinking three large supply ships that were all