Their bullet-riddled bodies were found on Wednesday in Vavuniya, a town in the north and close to the frontline with Tamil Tiger rebel-controlled territory.
The defence ministry said 10 Tiger rebels were killed in skirmishes with security forces in Mannar while another three were killed in Weli Oua on Tuesday.
The ministry did not say if troops suffered any casualties.
There was no immediate comment from the Tigers on the defence ministry claims. The latest killings came a day after the defence ministry reported 12 people were killed in two separate incidents in the northeast on Monday.
The violence followed an air attack by Tamil Tiger light aircraft in the capital Colombo.
A fuel storage tank owned jointly by the government and the Indian Oil Company was destroyed while two