The protesters say the bodies found in the mass grave are of ethnic Baluch men, allegedly abducted by state intelligence services.
Officials deny the claim.
The bodies -- most of them badly decomposed and beyond recognition -- were discovered by a local shepherd on January 25.
Officials say there were 13 bodies in the mass grave, while Baluch sources claim the number of bodies exceeds 100.
The Human Rights Commission of Pakistan has also questioned Pakistani authorities over the mass grave.
The region is the scene of a decades-old insurgency by Baluch nationalists, who are demanding greater autonomy.