The fishermen, hailing from Rameswaram and Mandapam, had been arrested while fishing near Katchatheevu, Rameswaram Fishermen's organisation president S Emerite said.
While 38 fishermenhave been lodged in Vavuniya prison, the six boys have been kept in a camp.
The fishermen were produced before the Mannar judicial magistrate court which extended their remand till April 12.