The fishermen from Tamil Nadu were arrested yesterday while fishing near Sri Lanka's Neduntheevu island, the navy said.
They were found illegally fishing in Sri Lankan waters northwest off the coast of Jaffna's Delft islet, it claimed.
Around 3,500 fishermen in 634 boats had put out to sea from Rameswaram last night.
The fishermen were detained and taken to Kangesanthurai Port along with their two boats, Tamil Nadu police and state Mechanised Boat Fishermen Association leader P Sesuraja said.
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The fishermen issue has become a flash point in India-Sri Lanka relations, with Indian fishermen facing Lankan navy action, including firing for alleged violation of the International Maritime Boundary Line (IMBL).
On November 4, India and Sri Lanka decided to set up a Joint Working Group (JWG) on Fisheries to meet every three months and hold a meeting between the Ministers for Fisheries every six months.
This was agreed during extensive talks in New Delhi between Ministers of External Affairs Sushma Swaraj and Agriculture Radha Mohan Singh with Sri Lankan Foreign Minister Mangala Samaraweera and Fisheries and Aquatic Resources Development Minister Mahinda Amaraweera on possible mechanisms to find a permanent solution to the emotive issue of fishermen.