The boats of the Liberation Tigers of Tamil Eelam were heading towards the northern port of Kankesanthurai at the northern edge of the Jaffna peninsula in an attempt to attack it, the ministry said in a statement.
Naval gunboats intercepted the Tiger boats leading to the battle, which lasted for six hours, it said.
"Twelve Sea Tiger craft, including five suicide boats, were destroyed killing over 80 Tiger terrorists and injuring many others on board," the ministry said. "The remaining craft left the area."