The Nowhatta area of Jammu and Kashmir capital resembled a battle zone as masked protesters burnt the tricolour and clashed with security forces resulting in injuries to about a dozen people, including two policemen, official sources said.
The protesters were also seen hurling stones at the police which retaliated, bursting teargas shells and using force to disperse the violent crowds.
Reports of stone-pelting were also received from Tral and adjoining areas as part of a march call given by hardline Hurriyat faction led by Syed Ali Shah Geelani. The moderate faction of the Hurriyat led by Farooq also staged its own protest.
Geelani has given a strike call throughout the Valley tomorrow against the killings and today's police action.
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Earlier in the day, Bhat, being seen as a possible successor to Geelani, was arrested following outrage over raising of pro-Pakistan slogans and flags at a rally on Wednesday where the two were present. Both leaders were placed under house arrest here late last night.
As the Centre came under attack for the situation in the state ruled by PDP-BJP coalition, Union Home Minister Rajnath Singh asserted India's unity and integrity were "inviolable" and "nobody will be allowed to break it".
"Anybody found engaging in anti-national activities will not be spared or forgiven," he told a press conference near Kanpur.