Sri Lanka's External Affairs Ministry said its navy had not been present at the two locations where it was accused of killing two Indian fishermen on two separate occasions this month.
"There were no Sri Lanka Navy vessels in the vicinity of the locations, where the incidents are alleged to have occurred," the Ministry said in a statement.
Earlier, Indian media reported that a man, who had put out to sea with two others on Saturday from Pushpavanam coastal hamlet, died after Sri Lankan Naval personnel tied a rope around his neck and pushed him into the water.
A similar allegation was levelled at the Sri Lankan navy early this month after another fisherman was killed in mid sea.
For this purpose, the Government of Sri Lanka has requested from the Indian authorities through diplomatic channels the fullest possible information.
The Ministry wishes to emphasise that as and when this information is made available, further investigations based on the additional data that may be provided, would be conducted.
It said it is the consistent policy of Sri Lanka to treat in a humanitarian manner all fishermen, including those from the Indian fishing community, who cross into Sri Lankan waters.
"In keeping with this policy, the Sri Lanka Navy has within the last 12 months afforded assistance to 32 Indian fishermen and 10 Indian fishing vessels," it said.
As soon as reports of the alleged incidents began to appear, the Sri Lanka Navy was instructed to carry out its own inquiry.
The government is accordingly most anxious to ascertain the facts behind the alleged incidents, so that any perpetrators are brought to account.
Earlier, strongly reacting to the killing of a second Indian fisherman in less than a fortnight allegedly by the Lankan Navy, New Delhi termed it as "unacceptable" and sought a report in the matter from its mission in Colombo.
External Affairs Minister S M Krishna in New Delhi had taken the matter "very seriously", saying it was "unacceptable", sources said.