The Sri Lankan High Commission said none of its naval craft fired at "any fishing vessel or any other object" Wednesday or Thursday.
The alleged incident reportedly took place off Kodiakarai in Tamil Nadu, a statement by the mission said.
But the Sri Lanka Navy voiced concern "over the large number of fishermen from southern India crossing the international maritime boundary line and fishing in Sri Lankan waters on a regular basis".
It confirmed the arrest of 16 Indian fishermen allegedly poaching in Sri Lankan waters off the island nation's northwest on March 3.
"The Sri Lanka Navy reiterates its commitment to not use force under any circumstances and extend humane treatment to all fishermen at all times," it said.
Tamil Nadu and Sri Lanka are separated by a narrow strip of sea.