Shops and other business establishments downed their shutters in Maisuma and Budshah Chowk after Malik's supporters came out on streets in protest, official sources said.
Supporters of the separatist leader were protesting against the government's move not to allow Malik to visit the earthquake-affected areas of Doda region from where he was pushed back to the Valley this morning, the sources said.
Additional police and paramilitary CRPF have been deployed in the area to maintain law and order, they said.
So far, there are no reports of anyone getting injured in the brief clashes.