More than 70,000 people have reportedly been killed in the conflict since 1989.
Meanwhile, authorities declared an indefinite security lockdown in parts of Srinagar and other major cities and towns across the Kashmir Valley starting Sunday, which marks the beginning of the Muslim fasting month of Ramadan. Bhat succeeded charismatic militant leader Burhan Wani after he was killed in a gunfight in July, which triggered months of anti-India protests in which almost 100 people died. Hundreds were blinded or maimed by the firing of government forces.
Reports said the three houses in the locality were completely damaged. According to the Army, Sunday morning's operation was the second biggest infiltration attempt foiled in the last one week.
No sooner the news about militant commander's killing spread out, spontaneous shutdown and clashes triggered in most of the towns including Srinagar, Pulwama and Anantnag.
Soon after the killings, stone-pelting protests have started at several places in the Valley.
He said as the security forces were closing on the house where the militants were hiding, the ultras opened fire.More news: Rafael Nadal warms up for French Open with victory in Madrid
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The operation was carried out, following an intelligence tip-off, on Bhat's hideout in the village, the police official said, adding that one of Bhat's fighters had also been killed in the overnight gun battle, which ended later in the day.
With the killing of civilian, the death toll in the daylong violence across the region has risen to nine.
Hizbul Mujahideen terrorist Sabzar Ahmad was among the terrorists eliminated by Indian Army.
Pakistan has urged global community particularly the United Nations, OIC, P-5 and human rights organizations to immediately stop the ruthless killing of defenseless Kashmiris in occupied Kashmir. Keeping this in mind, the state government has again banned 2G, 3G and 4G internet services.
"In their desperation to hide the reality of the indigenous uprising of young Kashmiris, including thousands of girls and boys, India is trying to equate it with terrorism".