The attack underscored the dangers authorities and aid workers face in helping victims in south-western Baluchistan province, where a magnitude 7.7 earthquake hit earlier this week.
Rescuers were still struggling to help survivors yesterday as the death toll from Tuesday's quake reached 355, with nearly 700 people injured. In the town of Arawan, about 100 protesters gathered around the district office to bring attention to the plight of those living in outlying villages who are still waiting for some help.
The area's medical infrastructure has struggled to care for the hundreds of injured who were crushed beneath mud brick houses when the quake struck.
That task has been made even harder by the danger from separatists in Baluchistan who have been battling the Pakistani government for years.
The militants fired two rockets at a helicopter carrying top Pakistani officials in charge of relief operations.
The separatists claim to have already given out relief supplies to people hit by the quake.
Many of the injured were ferried to the port city of Karachi, or Quetta, the capital of Baluchistan, for treatment.