The catch loaded in 50 boats was taken away by the personnel who also snapped the fishing net used by the fishermen, officials said.
Tension prevailed in the coastal villages at Rameswaram following the incident.
The fishermen had not ventured into the sea for the past one week in protest against levying of tax on prawn import by the United States.
The seafood exporters in Madurai are not willing to buy the catch from them after this move.