According to officials armed men opened fire over the personnel of law enforcement agencies during the search operation in Windar near the industrial district of Hub.
The law enforcement personnel killed four militants in retaliatory fire, while three miscreants fled from the scene.
Three FC members were also injured in the shootout.
The dead bodies of militants have been transferred to Karachi for autopsy and to complete other legal formalities.
The officials have said that a large quantity of arms and ammunition has been recovered from the killed accused.
FC and police have cordoned off the area for arrest of other miscreants.
Baloch militant groups have been engaged in an insurgency to press for greater autonomy, the right of local people on the natural resources and provincial revenues in the mineral resources rich southwestern province of Pakistan.