Officials said the injured were fishing inside Sri Lankan waters. However, fishermen claim that they were on the maritime border area when the incident occurred yesterday.
Assistant Director of Fisheries Mohan said these fishermen had used a particular fishing net banned by Sri Lankan government and that could also be the reason for the attack.
He said initial enquiry revealed that five fishermen were stripped off their clothes and thrown into sea. The Lankan naval personnel also threw the catch and the fishing net into the sea after the attack.
The incident would be taken up with Colombo through the Centre, fisheries officials said.
An official said the Sri Lankan naval force could have arrested those who crossed the maritime border as was done by the Indian Navy, instead of attacking them.