A fierce gunfight followed, police sources said. A house used by the militants was set ablaze by soldiers and another was blown up with heavy explosives, witnesses said.
"The operation ended after bodies of the two militants were recovered from the site and identified", the police officer said.
This is for the first time that state police has chose to approach Pakistani authorities to take back the body of a militant since the eruption of militancy in 1990 during which hundreds of Pakistani and other foreign militants were killed in encounters with security forces in the state.
Police and the Army have a very clear strategy and that is that the Army operations will continue.
"He was involved in planning of nearly all the major militant attacks in Valley including the attack on CRPF convoy at Pampore area in south Kashmir's Pulwama district previous year in which eight CRPF men were killed and about a dozen injured and the attack on BSF convoy at Udhampur in which two border guards and a militant were killed and 10 others injured", he said.
Large protests and clashes against Indian rule spread to several other places across Kashmir, including the Himalayan region's main city of Srinagar, as students boycotted classes and hit the streets.
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Residents in the old quarters of Srinagar, the main city in Indian-administered Kashmir, were ordered to stay indoors and obey the curfew as government forces patrolled streets lined with steel barriers and razor wire.
Meanwhile, the slain youth as laid to rest at his native village in Pulwama district during which the participants raised anti-India and pro-freedom slogans. The state government has closed all the colleges and schools in wake of the students protests. He had a reputation for being "a master of disguise" who escaped at least five previous military cordons. "He knew the territory like the back of his hand".
His death is one of the biggest blows to Kashmiri separatists since the death of another commander, Burhan Wani, in July previous year.
On Tuesday, Indian forces martyred two youth after destroying a building with chemical weapon, while another youth was martyred during firing on the people protesting against the killings in the area, the media service reported.
Anti-India sentiment runs deep in Kashmir's mostly Muslim population and most people support the rebels' cause against Indian rule.
Militant groups, including LeT, have for decades fought roughly 500,000 Indian soldiers deployed in the territory, demanding independence or merger with Pakistan.