The three boats of the fishermen, hailing from Pamban and Thangachimadom near here, were also seized by the navy personnel, Assistant Director of Fisheries Department D Gopinath said.
The fishermen were arrested while fishing near Katchatheevu, an islet ceded to Sri Lanka by India by two agreements of 1974 and 1976.
Tamil Nadu Chief Minister Jayalalithaa had earlier this month written to Prime Minister Narendra Modi, requesting him to act decisively to find tangible mechanisms to permanently resolve this vexatious issue, affecting the livelihood of lakhs of fishermen of the state.
Later, the fishermen were produced before a court in Mannar and remanded to judicial custody.
The Mannar Magistrate Court remanded them to judicial custody till May 11, official sources said.
A 15-year-old boy, among the 21 arrested, was sent to a government-run home, they added.