Pakistan Maritime Security Agency spokesman said the fishermen will be handed over to police in Karachi to register cases against them.
The fishermen from Tamil Nadu were later taken to Kankesanthurai in the island nation.
Arrest comes days after Rajapaksa ordered release of all detained fishermen in a goodwill gesture ahead of Modi’s swearing-in.
300 members of All Mechanised Boat Owners Association demanded the release of its fishermen and boats seized by the Sri Lankan Navy.
Navalmen also chased away another group of fishermen when they were fishing near Katchatheevu.
The Pune rural police on Monday arrested 12 persons suspected to be Bangladesh nationals who had been fishing in the waters of Ujani dam in Indapur for the last few months.