A team of forensic experts led by Judicial Medical Officer Dhananjaya Waidyaratne has so far found skeletal remains of at least 36 individuals in the grave.
"The bodies have been buried in several layers," Waidyaratne told BBC's Sinhala Service in Mannar's Thirukatheeswaram area.
"It is difficult to place a time of death or a cause of death without further scientific tests," he said.
Workers of a state water entity stumbled on the grave while digging the ground to lay water supply pipes late in December.
More From This Section
Police said in an initial reaction that the site had been under LTTE control for well over 15 years.
"It was possible that the victims might be those abducted and killed by the LTTE during their violent separatist campaign," police spokesman Ajith Rohana said.
Tamil rights groups, however, said the remains were those of Tamil civilians who disappeared during the conflict.
This was the first mass grave found in the former conflict zone since the war ended over four years ago.
The UN Human Rights Council has passed two resolutions against Sri Lanka and a third one is expected in March.