The case is deeply divisive in the volatile Kashmir Valley, which lies at the heart of the rivalry between India and Pakistan. The two have been to war twice over the province, which was divided between them when British India was partitioned in 1947. Many Kashmiris reject the territorial claims of both countries and want independence.

The delicacy of the case was on display in the courtroom here. When officials from the Central Bureau of Investigation began to give a presentation for the judges, the women’s relatives shouted accusations of a cover-up. They shouted their suspicion that the women had been abducted while returning home from the family orchard on the outskirts of the town of Shopian and then raped and killed.

The agency filed charges against 13 people, including 6 doctors, 5 local lawyers, an activist and the brother of one of the dead women. The charges included fabricating evidence and intimidating witnesses after the recovery of the two bodies.

Speaking to reporters after his presentation of the evidence in court, Anil Bhan, a lawyer for the Central Bureau of Investigation, said that the bodies of the women were exhumed in the presence of their family members, that a medical inspection showed that Ms. Jan had not been raped, and that the evidence indicated that she was a virgin when she died. He added that experts from the All India Institute of Medical Sciences, India’s elite medical school, had completed the examination.

An autopsy report prepared by local doctors said that the women had been raped before they were killed. But the Central Bureau of Investigation report says the doctors gave false post-mortem reports and sent slides for DNA examination that had been tampered with.

“It now seems that whole charade of investigation by multiple agencies, one after the other, was aimed at shielding the culprits rather than bringing them to book,” said Mehbooba Mufti, the president of the opposition People’s Democratic Party. She described as “cruel irony” the move to file charges against “the family, the witnesses, lawyers and those who have wanted justice to be done.”