"We have not allowed fishing in our waters for the Indians. I have given clear instructions to navy to arrest boats or trawlers that violate our water limits," Sirisena told a gathering of fishing industry and political representatives last night.
Opposition group National Freedom Front had alleged that the government had given fishing rights to Indians in Sri Lankan waters as an appeasement policy towards India.
"We have asked the Indians to stop bottom trawling," Sirisena said.
The President said he was looking forward to a constructive role by the Tamil-ruled northern provincial council to resolve the dispute.
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"I hope they can exercise their legislative powers to tackle the issue even by consulting the Indian High Commissioner (Ambassador)," Sirisena said.
The two countries held fishermen-level talks in Chennai last month. The Indian fishermen had reportedly called for 83 days per year for three years to fish in the Palk Strait, the narrow sea strip separating the two countries.
However, there was no official communique on the talks.