Navy spokesman Kosala Warnakulasuriya said that the Indians were arrested last night for "poaching inside Sri Lanka international maritime border limits (IMBL) off the eastern coast".
The boats and the trawlers would be handed over to the police in the harbour town of Trincomalee today for further action, the Navy said.
Early this month, at least 40 Indian fishermen and their four trawlers were repatriated by the Navy after a similar arrest for straying into Sri Lanka's IMBL.