Ten trawlers of the fishermen were also seized by the Sri Lanka Navy on Wednesday.
Sri Lankan Navy spokesman Kosala Warnakulasuriya said 49 fishermen had been arrested on two separate occasions off the northern coastal areas of Kankesanturai and Talaimannar.
While 24 of them were handed over to the Talaimannar police on Wednesday the rest of them were to be handed over to the Kankesanturai police on Thursday.
They will be produced in court and charged for violating Sri Lanka's international maritime border line, the Navy said.
The issue of fishermen continues to be thorny in the relations across the Palk Straits as the Sri Lankan Navy is often accused of harassing the Tamil Nadu fishermen.
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