Asked how the issue would be resolved in the light of disagreement at today's talks, Rajapaksa said the matter would now be thrashed out at the high-powered committee manned by three officials from each side.
Rajapaksa said the six-member committee is expected to meet next month in order to find a permanent solution to the fishing issue between the two countries.
The committee was appointed as a result of the talks between the Sri Lankan fishing minister Rajitha Senaratne and his Indian counterpart, Sharad Pawar early this year.
Today's talks, which were scheduled to take place in mid-March, did not take place as the Tamil Nadu government protested the detention of Indian fishermen by Sri Lanka.
The Tamil Nadu government had demanded the release of all Indian fishermen before the talks could resume. Sri Lanka had seized over 160 fishermen despite the agreements reached at talks held in Chennai in January.