Two human rights groups have accused the Indian government of an “institutional cover-up” to avoid punishing dozens of high-ranking military and police officials implicated killings, disappearances, torture and sexual violence in the disputed Himalayan region of Kashmir.

A report by the International Peoples’ Tribunal on Human Rights and Justice in Kashmir and the Association of Parents of Disappeared Persons (APDP) has identified more than 900 individuals whom it blames for a range of human rights abuses carried out by Indian security forces between 1990 and 2014. They include 150 officers of the rank of major or above.

“The people alleged to be involved in these crimes cannot commit them individually. Others will have supported them or could have stopped them. We looked at officers at a higher level who knew about the human rights abuses. This was a systematic tactic and policy,” said Khurram Parvez, one of the report’s authors.

Kashmir was split between India and Pakistan when the two nations gained their independence from Britain in 1947. From the late 1980s until today a brutal insurgency has pitted Indian security forces and police against Islamic militants, some backed by Pakistan, and separatists in the former princedom.

Tens of thousands have died in the conflict, mainly civilians, and both sides have committed serious human rights abuses.

In recent years the violence has declined, but the dispute over the region continues to fuel deep animosity between the two nuclear-armed neighbours, while many Kashmiris continue to demand independence from both, or at least a greater degree of autonomy.

There have long been allegations of torture and arbitrary detention by Indian security forces during the conflict. In 2010, leaked diplomatic cables revealed a briefing by the the International Committee of the Red Cross to US officials that details a range of abuses in detention facilities run by the Indian army as well as by local police and paramilitaries.

A relative of Auqib Ahmad Bhat mourns on seeing his dead body during his funeral in Balpora. According to relatives, Bhat, 22, who was a water-tanker driver ferrying water to Indian army camps, was beaten to death by Indian paramilitaries. However, police have denied the charge and say he was killed in a road accident. Photograph: Yawar Nazir/Getty Images

Last week six soldiers, including a colonel and a captain, were given life sentences by a court martial for their role in the 2010 killing of six local Kashmiri civilians, whom they had falsely claimed were extremist infiltrators in order to gain a cash reward. The incident prompted widespread rioting and anger.

Some have seen the judgment as part of an effort to change local perceptions of the Indian security forces in Kashmir.

Ajai Shukla, a military analyst and former officer who served two terms in Kashmir, said: “The fact that the army has court-martialled mid-ranking officers is a hopeful sign of a changed approach. It does not mean the velvet glove is replacing the iron fist entirely but shows a recognition that it cannot be business as usual with human rights violations covered up.”

Parvez, of the Kashmir group, said it was too early to judge the impact of the recent convictions. “In other cases there have been similar judgments but they have been quashed on appeal and the men involved reinstated. We will have to see what happens now,” he said.

The report documents the extrajudicial killings of 1,080 people and enforced disappearances of 172 people in detail as well as further cases of torture and sexual violence. It identifies 972 individual perpetrators, including hundreds of paramilitaries and auxiliaries who worked alongside military forces.

Shukla, the former soldier, said human rights groups were not sufficiently sceptical of accounts given by victims or their relatives in an environment polarised by decades of conflict.

A spokesman for the Indian army in Kashmir said he had no comment to make on allegations of human rights abuses by military personnel.