The bodies were found last week on a small island about an hour's boat ride from the capital of Nuku'alofa.
Photos show the carcasses washed up onto the beach and nearby rocks.
Prison officer Kolianita Feke told Yahoo7 he stumbled upon the whales' remains.
"Early in the morning we walked around the island and saw them, but they were already dead for a few days," Mr Feke said.
"They were shot with a gun. It looked like they had a hole near the head area, or near their mouth."