More than 2,000 corpses, believed to be victims of Kashmir's long-running insurgency, have been found buried in dozens of unmarked graves in the divided region, an Indian government human rights commission report has said.

The graves were found in dozens of villages on the Indian side of the line of control, the de facto border that has split the former kingdom between India and Pakistan for nearly 40 years.

"At 38 places visited in north Kashmir, there were 2,156 unidentified dead bodies buried in unmarked graves," the inquiry found.

Though campaigners and community leaders in Kashmir have long said such graves exist – and often provided extensive documentary evidence to back up their claims – the report is the first official statement confirming their existence.

Released over the weekend, its publication is the result of a three-year inquiry by an 11-member team led by a senior police official.

Up to 70,000 people died in the 22-year insurgency in Kashmir, which pitted armed separatist groups, many backed by Pakistan, against New Delhi's rule.

The worst of the violence occurred during the mid-1990s when a vicious struggle pitted thousands of militants against Indian security forces supplemented by locally-hired irregulars. Human rights abuses were routine with militants intimidating local communities and killing so-called spies while Indian authorities resorted to abductions, torture and extra-judicial executions on a wide scale. The graves appear to date from this period.

Kashmir is India's only Muslim-majority state and the struggle rapidly took on a religious dimension. The victims in the mass graves had been buried by local communities.

Police originally described the bodies to villagers as "unidentified militants". This claim is disputed by the report, local media said , which also calls for a forensic investigation involving DNA identification of remains.

Investigators spoke to former police officials, village heads, clerics, gravediggers and cemetery caretakers, the Indian Express newspaper reported.

Though violence has declined dramatically in recent years, in part due to a peace process between India and Pakistan, clashes still occur. On Saturday, Indian soldiers shot dead 12 separatist militants trying to cross from Pakistan into the disputed region. An Indian officer was also killed in the incident.

One frequent accusation is that Indian security forces in Kashmir have killed innocent civilians in staged gun battles and passed them off as separatist militants to earn rewards and promotions. One such alleged incident last year provoked rioting throughout most of the summer.

This summer, however, has proved relatively quiet with tourists returning to the region.

Indian authorities have consistently denied systematic human rights violations in Kashmir and say they probe all such reports and punish the guilty.

A US diplomatic cable leaked by WikiLeaks and published by the Guardian last December revealed a briefing to the US embassy in Delhi by representatives of the International Committee of the Red Cross which described continuing torture and arbitrary detention by security forces.

The Association of Parents of Disappeared Persons, which estimates around 10,000 people have gone missing in the past 20 years, says many may have ended up in these unmarked graves. "We appeal to international human rights groups and Indian authorities to identify the people buried," said Parveena Ahanger, founder and chair of the group. International human rights groups have also repeatedly asked the Indian authorities to investigate the unmarked graves.