The fishermen, from Thondi in Ramanathapuram District, were fishing in a mechanised boat when they were surrounded by the Sri Lankan Navy men and thrashed with sticks.
They also cut their fishing nets and dumped their catch into the sea, besides snatching their GPS equipment and cell phones, the officials said adding the fishermen were detained for more than two hours.
The fishermen arrived at Rameswaram on Monday night and were treated as out-patients and given some pain killers and ointment by local doctors, they said.
The alleged attack comes after a brief lull in such incidents. In a welcome gesture, Sri Lankan Naval personnel, had on January 24 offered refreshments to a group of fishermen from Rameswaram when they were fishing near Katchatheevu.
Minister of State in PMO V Narayanasamy had last month said India and Sri Lanka were close to clinching an agreement on drawing a fishing boundary in the Palk Strait to avoid incidents of attacks on Tamil Nadu fishermen.