The fishermen were produced before the Mannar and Trincomalee Magistrates' Courts yesterday.
They were arrested by Sri Lankan on June 19 from two different locations in the country.
Twenty two of the fishermen will remain in judicial custody until June 27 while 24 others have been remanded till July 2, officials said.
Sri Lankan Navy personnel had arrested 82 fishermen on June 7 after they allegedly entered the island nation waters. However, they were ordered to be released by President Mahinda Rajapakse in a goodwill gesture.