A division bench of the court here comprising Justices A Selvam and Athinathan gave the direction on a PIL filed by D Raju.
The bench said the 22-year-old fisherman Bridgo had been allegedly shot dead on the high seas and sought to know whose jurisdiction it was to investigate the "murder".
It asked whether it was the responsiblity of the Indian Coast Guard or Sri Lankan authorities to apprehend the accused or should some international body find the accused. It asked the Centre to clarify the matter.
He alleged that 600 Indian fishermen had been shot dead so far and no accused arrested.
Bridgo was shot dead on March 6, allegedly by the Sri Lankan navy, while he was fishing in a mechanised boat at a short distance from Katchatheevu islet. Another fisherman had been injured in the incident.
Subsequntly, a case was registered against the Sri Lankan Navy, based on a complaint from a fisherman.
Raju alleged that though the fishermen had been shot dead in Indian waters near Adam's bridge, the accused had not been arrested by the Indian authorities.
The petitioner sought a direction from the court to the Central government officials, including secretaries of Home and External Affairs Ministries, besides Tamil Nadu Chief Secretary to take action in the matter.
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