Rights group Human Rights Watch has urged India to hold an independent inquiry into the unmarked graves found in Indian-administered Kashmir.
Earlier, the state human right commission said it had evidence that 2,156 bodies had been buried in 40 graves over the last 20 years.
The commission is the first government body to confirm what others have previously alleged.
Its report is yet to be submitted but it has been widely leaked in the media.
The commission's investigation focused on four northern, mountainous districts and involved scrutinising police, mosque and graveyard records, interviewing police and local people and cross-referencing information.
"For years, Kashmiris have been lamenting their lost loved ones, their pleas ignored or dismissed as the government and army claimed that they had gone to Pakistan to become militants," Meenakshi Ganguly, South Asia director at Human Rights Watch, said.
"But these graves suggest the possibility of mass murder. The authorities should immediately investigate each and every death."
Independent human rights groups have long insisted that thousands of people have mysteriously disappeared over the last two decades and never been accounted for.
Some have accused India's security forces of abducting local people, killing them and covering up the crime by describing the dead as unknown militants when they are given for burial.
The authorities deny such accusations.
The security forces say the unidentified dead are militants who may have originally come from outside India.
They also say that many of the missing people have crossed into Pakistan-administered Kashmir to engage in militancy.