Senior NC leaders Ali Muhammad Sagar and Chowdhary Muhammad Ramzan led over three dozen party workers who were protesting against the use of pellet guns by security forces for mob control in the Valley.
The party men also shouted slogans against alleged failure of the state government in handling the ongoing unrest.
Police later intervened to disperse the protest.
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The civil secretariat houses the offices of the Chief Minister Mehbooba Mufti, her cabinet colleagues and all top bureaucrats of the state.