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However, the Sri Lankan envoy denied involvement of his country`s Navy in the killing of the fisherman on Wednesday.
Meanwhile, External Affairs Minister S M Krishna has sought a detailed report from the Indian High Commissioner in Colombo, who has taken up this matter with the Lankan government and expressed "deep concern and regret" over it.
In a fresh incident of attack on Tamil Nadu fishermen in Palk Straits, one person was killed when Sri Lankan Navy allegedly opened fire at three fishermen, who put out to sea from Jagadapattinnam near Pudukottai.
Emphasising that resorting to firing in these situations has "no justification", India called on the Sri Lankan authorities to "desist" from use of force.
The Government summoned Kariyawasam to the MEA where the Joint Secretary in the division dealing with Sri Lanka registered India`s strong protest.
Kariyawasam denied the involvement of Lankan Navy in the incident but said Colombo will conduct an inquiry since India had officially informed about it.
"Our enquiries reveal that the Sri Lankan Navy is not involved. The Navy is under strict orders never to fire at fishermen even if they cross international boundary line towards Sri Lanka," Kariyawasam told reporters after the meeting.
He said investigations will happen in Lankan side and Indian side as well to find out what exactly happened.
"But my information at this point from our Navy is that their vessels were not in that area...But nevertheless we will conduct an inquiry since we have been officially informed about this incident," he said.
Asked whether the incident happened on Sri Lankan side, he said their Navy never crosses into Indian waters "but as you know Indian fishermen sometimes crosses the boundary line and fish in our waters".
The MEA said, "we have consistently emphasised to the Sri Lankan Government to refrain from firing on our fishermen and scrupulously adhere to the October 2008 understanding reached between the two governments. We call on the Sri Lankan Navy to exercise maximum restraint and avoid use of force in such situations."
