Allah Nazar, chief of the banned Baluch Liberation Front (BLF), is believed to have been killed in a raid last month, Baluchistan Home Minister Sarfraz Bugti told a news conference in the provincial capital of Quetta.
Separatists have been waging a low-intensity insurgency in poverty-racked Baluchistan for decades, demanding an end to what they see as the exploitation of their gas and mineral resources by people from richer, more powerful parts of Pakistan.
The rebels have carried out frequent kidnappings and killings, including the execution of 20 labourers in April, and they often attack gas pipelines and other infrastructure.