The defence ministry said in a statement that the rebels had buried 74 of their cadres and that 27 dead were lying along the frontline near the port.
It also said that the bodies of 16 dead rebels had been returned since fighting began Sunday.
Separately, military sources said 15 soldiers were killed and another 92 wounded.
The Tigers said that they had stalled military's air and ground offensive towards the rebel-held town of Sampur, about 10 kilometres (six miles) from Trincomalee, which has been used as a staging post to mount artillery attacks.
The pro-rebel Tamilnet website said the Tigers had killed at least 50 soldiers and lost 18 of their own men.
It accused the military of killing 20 civilians in a shell attack.
"The Sri Lanka army has intensified artillery and mor