More than 2,000 bullet-riddled bodies were found buried in dozens of unmarked graves across Kashmir, an Indian government human rights commission inquiry has concluded.

The inquiry, is the result of three years of investigative work by senior police officers working for the Jammu and Kashmir State Human Rights Commission, and constitutes the first official acknowledgement that civilians may have been buried in mass graves in Kashmir.

Many of the bodies recovered had multiple bullet wounds and are thought to be those of civilians who disappeared more than a decade ago during a brutal insurgency that swept the region.

Since India and Pakistan gained their independence in 1947, both countries have been at war twice over Kashmir, and the territory still continues to be a source of tension between the nuclear-armed neighbours.

Separatist rebel groups began an insurgency against India in 1989 and tensions rose after India accused Pakistan of arming and training militants.

The inquiry was launched following allegations of widespread human rights abuses by the Indian army, paramilitary and police, which the Indian government had until now mainly denied, saying that the bodies were militant fighters who fought the government.

The new report however has shed light on the conflict as it seems to confirm that many civilians were also killed as a result of the confrontations.

According to the 17 page document 2,156 unidentified bodies were found in graves in three northern mountainous regions and the report says "there is every possibility that.... various unmarked graves at 38 places of North Kashmir may contain the dead bodies of locals".

"There is every probability that these unidentified dead bodies buried in various unmarked graves at 38 places of North Kashmir may contain the dead bodies of enforced disappearances," the report said.

Among the corpses, 574 other bodies have already been identified as local people.

According to the International People's Tribunal on Human Rights and Justice 8,000 people have gone missing during the 20-year rebellion against Indian rule over the territory with many of them going missing after being in the hands of the Indian security forces.

India, on the other hand has insisted those gone missing had crossed to Pakistani administered Kashmir to train with terrorist groups.

The reports now calls for a thorough inquiry and collection of DNA evidence to identify the dead, and urged for better identification of the people killed by the security forces in Kashmir to avoid abuse of special laws protecting the military from prosecution there.