Indian Home Minister Amit Shah said the three men were Pakistani nationals who were killed in a joint operation by the military, paramilitary and police on Monday on the outskirts of Kashmir's main city of Srinagar.
Shah made the remarks in India's lower house of the parliament, and The Associated Press could not independently verify the details.
Shah said the bodies of the men were identified by people who had provided food and shelter to them before they carried out the massacre in April.
He cited a forensic report and said the rifle cartridges found at Monday's gunbattle site matched those used during the attack.
The April gun massacre killed 26 people, mostly Hindu tourists.
New Delhi blamed the attack on Pakistan, which denied responsibility while calling for a neutral investigation.
It led to tit-for-tat military strikes by India and Pakistan that brought the nuclear-armed rivals to the brink of their third war over the region.
Dozens of people were killed on both sides until a ceasefire was reached on May 10 after US mediation.
The four-day fighting between the nuclear-armed rivals was their worst in decades.
Before the April gun massacre in the Kashmiri resort town of Pahalgam, fighting had largely ebbed in the region's Kashmir Valley, the heartland of anti-India rebellion and mainly shifted to mountainous areas of Jammu in the past few years.
India and Pakistan each administer part of Kashmir, but both claim the Himalayan territory in its entirety.
Militants in the Indian-controlled portion of Kashmir have been fighting New Delhi's rule since 1989.
India describes militancy in Kashmir as Pakistan-backed terrorism, which Pakistan denies.
Many Muslim Kashmiris support the rebels' goal of uniting the territory, either under Pakistani rule or as an independent country.
Tens of thousands of civilians, rebels and government forces have been killed in the conflict.
