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.
Violence erupted after authorities denied permission to the hardline Hurriyat faction led by Syed Ali Shah Geelani to hold a march from Srinagar to Tral to protest the killing of two youths in an army operation earlier this week.
Moderate Hurriyat leader Mirwaiz Umar Farooq, who led a march in Tral accused the army of killing youths after labelling them terrorists. "There is no arrest, no FIR. The government has to put an end to state terrorism," he said.
Reports of stone-pelting were also received from Tral and adjoining areas.
Geelani has given a strike call throughout the Valley tomorrow against the killings and today's police action.
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.
The 45-year-old hardliner was arrested from his home in Habbakadal area of the city this morning, apparently after the Centre pushed for it.
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.