The suspected mass grave in the northeastern district of Mannar is the first one found after the end of the military campaign against the LTTE four years ago.
"A magisterial inquiry will begin tomorrow after the discovery of four more skulls," said Senior Superintendent Ajith Rohana, a police spokesman.
On Friday, workers of the National Water Supply and Drainage Board found skeletal remains when they were digging to lay water pipes adjacent to a road in Mannar, Rohana said.
Rights groups had highlighted the existence of mass graves in the north during the three-decade separatist campaign.
A similar mass grave was found outside the battle zone in the central district of Matale last year.
The Marxist JVP claimed the victims in that grave were its members who had allegedly died at the hands of security forces during 1987-90 when the party led an insurrection against an intervention by the Indian government in Sri Lanka's separatist conflict.