The Navy spokesman Akram Alavi said that 78 of them were handed over to the Indian coast Guards vessel 'sagar' off the coast of Kankesanturai while the remaining were handed over to the Indian vessel 'Raj Kamal' off the coast of Talaimamnar in the north.
Sri Lanka and India had agreed to release fishermen in mutual custody following talks between the authorities.
Sri Lankan fisheries minister Mahinda Amaraweera said that although the fishermen will be released their equipment will remain confiscated.
Fishermen violating each other's territorial waters has become a thorny issue in the Indo-Lanka relations.
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Sri Lanka accuses Indian fishermen of straying into its territorial waters, while the latter maintain they are only fishing in their traditional areas, especially around Katchatheevu, an islet ceded to Colombo in 1974.
The issue of poaching by each other's fishermen has been recurring despite some top level engagements between the two countries since the beginning of 2014.
The two countries have held top ministerial level talks in this regard and the issue figured in Prime Minister Narendra Modi's visit to Sri Lanka early this year.