No fisher was injured in the incident, they said.
The naval personnel allegedly surrounded the boats, pelted stones, threw bottles and iron pieces and damaged about 20 fishing nets, they said.
The fishers were also warned not to venture near Katchathivu, an islet ceded to Sri Lanka by India in 1974, they added.
The officials said about 2,000 fishers had put out to sea in the Palk Straits in 645 boats.