Massive anti-India protests and clashes erupted in India-held Kashmir after a top commander from the largest separatist group in the disputed region was killed in a gun battle with government forces on Saturday.

Sabzar Ahmad Bhat, head of the Hizbul Mujahideen separatist group, was killed in an overnight gunfight in Tral area, some 40 kilometres south of Kashmir's capital, Srinagar.

Hizbul Mujahideen is the largest indigenous separatist group fighting against Indian-rule in the Himalayan territory since an armed rebellion broke-out in 1989.

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One of Bhat's fighters was also killed in the gun battle, which erupted late Friday after government forces cordoned off a village following an intelligence tip-off.

“Yes, both of them were gunned down and the operation is still going on,” police chief Shesh Pal Vaid told AFP.

As the violence raged, hundreds of angry residents chanting anti-India slogans marched in an attempt to help the trapped separatists escape.

Clashes between rock-throwing protesters and government forces erupted in different places in the area, with police and paramilitary soldiers firing shotgun pellets and tear gas to stop the protests.

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As the news of the separatist leader's killing spread in the region, thousands of people, including students, took to the streets shouting “Go India, go back” and “We want freedom”.

Traders shuttered shops and businesses across the Kashmir Valley, including in Srinagar. Officials said clashes were reported from over four dozen places in the region.

Police said hundreds of villagers tried to break the cordon by throwing rocks at security forces, resulting in clashes that left at least 10 injured.

Authorities suspended most internet services in the region a day after they lifted a month long ban on 22 social networking sites, including Facebook and Twitter.

The social media ban on April 26 came after videos depicting the alleged abuse of Kashmiris by Indian forces fueled widespread protests.

Bhat succeeded charismatic separatist leader Burhan Wani after he was killed in a gunfight in July 2016, which triggered months of anti-India protests in which nearly 100 people died.

Wani's popularity grew after he used social media to attract new recruits for his militant outfit.

On Saturday, in a separate incident, the Indian army claimed they had killed six alleged militants who had infiltrated across the border from Pakistan in the Himalayan region.

Pakistan condemns killings, urges UN to intervene

Foreign Affairs Adviser Sartaj Aziz strongly condemned the killing of 12 youngsters in India-held Kashmir and urged the United Nations and the international community to bring an end to the bloodshed in held Kashmir, said a statement issued from the Foreign Office.

"Aziz strongly condemned killing of 12 people in held Kashmir since yesterday by the Indian forces in Pulwama and Baramulla," the statement said, adding that three of them were "martyred extra-judicially".

The adviser urged the global community, particularly the UN, Conference of Islamic Countries, P-5 members and human rights organisations to call upon India to immediately stop the killing of defenceless Kashmiris, it added.

"India has been heightening tension at the LoC to hide these crimes against the innocent Kashmiris being perpetrated with impunity," Sartaj Aziz said.

"In their desperation to hide the reality of the indigenous uprising of young Kashmiris, including by tens of thousands of girls and boys, India is trying to equate it with terrorism," he was quoted as saying.

He added that India’s plan to gradually change the demography of the India-held Kashmir to convert the majority Kashmiri people into minority has been brought to the attention of the United Nations Security Council.

Aziz reaffirmed the government and the people of Pakistan’s unflinching support for their Kashmiri brethren in IoK in their just struggle for the right to self-determination as promised to them in the relevant UN Security Council’s resolutions on Kashmir.

Anti-India sentiment runs deep in the predominantly Muslim Kashmir valley, one of the world's most heavily militarised areas, where most people favour independence or a merger with Pakistan.

Several armed rebel groups are fighting against Indian rule, with tens of thousands of people, most of them civilians, killed in the nearly three decades-old conflict.