The army said it killed three rebels April 30 who had crossed into Indian Kashmir from the Pakistani side in Machil, an area near the highly militarized cease-fire line between the rival nations. The army also claimed to have seized five assault rifles and ammunition after the gunbattle.
However, villagers and relatives of three Kashmiri men who had gone missing from Nadihal village three days before the purported gunbattle grew suspicious and organized massive protests after a photograph published in newspapers earlier this week matched one of the missing men, said resident Bashir Ahmed.
Omar Abdullah, Indian Kashmir's top elected official, ordered an investigation and police on Friday exhumed the bodies.
"The bodies were handed over to their relatives after their identification and fresh medical examination," said police officer Mohammed Yousuf.
Indian army spokesman Col. Vineet Sood said the army was awaiting the results of the police investigation. "Army is concerned about the seriousness of the allegations. In case any wrongdoing is established, action will be taken against the guilty," he said.
Anti-Indian sentiment runs deep in Kashmir, where government forces are often accused of killing and torturing people they suspect to be tied to militants and also for wining rewards and promotions. Authorities routinely investigate such allegations, but rarely prosecute those involved.
Rights groups in the past have often dismissed government probes as a public relations tool aimed at calming public anger.
Separatists have been fighting since 1989 for Kashmir's independence from India or its merger with neighboring Pakistan. More than 68,000 people, most of them civilians, have been killed in the uprising and subsequent Indian crackdown.
