In the morning, bodies of two militants - one foreign and one local Jaish militant - were recovered.
The gunfight started on Monday evening after the armed forces launched an operation in Batmuran village of the district.
The encounter continued throughout the night after the 44RR, 14 Bn of CRPF and SOG cordoned off the area after inputs about presence of three militants in Batmuran.
Police said security forces opened fire after they came under intense stone pelting.
A woman was killed during anti-India protests in disputed Kashmir on Tuesday following a gunbattle that killed two rebels, police and villagers said. The government forces responded with bullets and pellet fires.
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The trapped militants tried to escape while firing their guns but soldiers retaliated, leading to a prolonged clash. The bullet hit youth were identified as Ajaz Ahmed Dar son of Ghulam Muhammad of Batapora, Jahangir Ahmed Wani son of Ali Muhammad, a resident of Wathoo, Feroz Ahmed Lone son of Abdul Rehman of Ganapora, Farooq Ahmed Ganai son of Muhammad Abdullah and Showkat Ahmed Paswal son of Nazir Ahmed, both residents of Bhattipora Shopian.
The identity of the militants is being ascertained, said the police.
In yet another bloody clash between civilians and the military on the Indian side of Kashmir, one woman has died and several other people have been injured in the Shopian district. "A lady with a bullet injury in her abdomen was brought to our hospital who was referred to SMHS hospital in a critical condition, " he added. Police further said that " as cordon was strengthened the civilians of nearby area were evacuated".
Two force personnel including an army man and a police man were also injured during the encounter.