SRINAGAR: Indian police said that a top Kashmiri separatist leader has been arrested for leading an anti-India protest march and raising pro-Pakistan slogans earlier in the week.

Police officer K. Rajendra said Masarat Alam was arrested Friday under India's unlawful activities act.

He said police put two other separatist leaders, Syed Ali Geelani and Mirwaiz Umar Farooq, under house arrest to prevent them from leading a planned march Friday to protest the killing of a militant commander's brother in India-held Kashmir.

The Indian army said the man was killed in a gun battle along with another militant on Monday, while his relatives and angry locals said he was tortured to death.

Read: Kashmir's chief minister calls waving of Pakistani flag 'unacceptable'

The chief minister of Indian-held Kashmir (IHK), Mufti Mohammad Sayeed, termed the waving of Pakistani flag at a Hurriyat rally as 'unacceptable', saying "it was illegal and could not be tolerated", according to reports by Indian media.

Masarat Alam, a likely successor to Hurriyat leader Syed Ali Shah Geelani, had organised a rally in the restive summer capital of Indian-held Kashmir. The rally, which was attended by thousands, was held as a show of strength to welcome Geelani on his return from New Delhi.

However, hours after the rally, the chief minister received a call from Indian Home Minister Rajnath Singh who demanded 'immediate and strict action' against the Hurriyat leader's demonstration. He also said that there could be no compromise on national security, as politics could not impinge on national security.

Read more: Kashmiri leader waves Pakistani flag at rally in Srinagar

Wahid Rehman Parra, youth president and spokesperson of Mufti Sayeed's People's Democratic Party, had said that 'separatists' cannot be denied the political space any longer.

"Separatism and Pakistan constituency in Kashmir is a reality and we have to deal with it. We can't deny democratic space to these people. It is an ideological battle now. We have to make them mainstream by giving them democratic space,"

India reacted furiously following the show of support for Pakistan at the Srinagar rally.

Masarat Alam was released from prison after four years on March 7 this year. The move drew a negative response from Indian Prime Minister Narendra Modi who said “I am angered and condemn the release, just like other lawmakers".

Know more: Release of Kashmiri separatist leader creates hurdles for Modi

Modi's Hindu nationalist BJP wants to bring the contested region into the Indian mainstream, while its regional partner, the PDP, supports self rule.

Violent protests erupt after Masarat Alam's arrest

Demonstrators set fire to an Indian flag and hurled rocks at riot police in Srinagar on Friday, as protests over the arrest of the separatist leader turned violent.

Hundreds took to the streets of Srinagar, capital of Indian-administered Kashmir, to vent their anger at Masarat Alam's detention.

The violence erupted soon after worshippers emerged from Friday prayer services in the city's mosques, chanting pro-Pakistan slogans and “we want freedom”, according to an AFP reporter on the scene.

The police tried to disperse the crowds by firing tear gas and then wielding their batons.

At least 16 people were injured during the clashes, including three policemen, an officer who was not authorised to speak to the media told AFP on condition of anonymity.

"He [Alam] has been arrested after a case for unlawful activity was registered against him,” K. Rajendra, the state's director general of police, told AFP.

The case stems from a rally on Wednesday organised to welcome another separatist leader, Syed Ali Geelani, on his return to Srinagar from New Delhi where he had spent the last three months receiving medical care.

Although that rally passed off peacefully, television images of Alam leading a chorus of his supporters chanting “jeeve jeeve Pakistan (long live Pakistan)” and other slogans against India's rule of the disputed region triggered widespread condemnation from politicians and the media.

Kashmir has been rocked by violent protests this week after the brother of a top rebel leader was killed by the army near the town of Tral in the south of the Kashmir valley.

Kashmir is divided between India and Pakistan since the two countries gained independence in 1947. Both claim the territory in its entirety. Although several rebel groups have been fighting Indian forces since 1989 for independence of a merger of the territory with Pakistan, street protests have become the principle mode of opposition to Indian rule.