India was among the 12 countries that abstained while the resolution moved by the US government was carried with 24 votes in favour.
India had voted in favour of two previous US-backed resolutions in 2012 and 2013.
The bilateral talks began in mid January to find a solution to the fishermen issue that often boils into a major political controversy in India.
Tamil Nadu Chief Minister J Jayalalithaa had demanded the release of all Indian fishermen held by Sri Lanka before the talks could resume.
Sri Lanka had seized over 160 fishermen despite the agreements reached at talks held in Chennai in January.
