Provincial Home Minister Mir Sarfraz Bugti told media that the forces went into action in Darijan area of Dera Bugti, some 250 kilometres southeast of Quetta, after reports suggested that the insurgents were hiding there.
He said security forces killed at least 30 members of the Baluch Republican Army (BRA), including two commanders, in the gunbattle.
The BRA wants to stop what they say is exploitation of the natural resources of the province and alleged rights abuses.
Bugti said that eight hideouts of the militants were destroyed in the operation and about 350 kilogrammes of explosives, 300 kilogrammes of landmines, 50 anti-personnel mines, arms and huge cache of ammunition were seized.
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"During the search operation the forces also managed to secure release of two hostages who were in custody of these militants," he said.
The identities of those killed were not known but Baloch nationalists frequently fight with forces in the restive province.
Bugti said the search operation was carried out in response to militant attacks against vital national installations and security forces.