"The court has dismissed all the charges against former ruler Pervez Musharraf and all those named in the case," Aftab Sherpao, a former interior minister also named in the case, told media in the southwestern city of Quetta, AFP reported.
The anti-terror court's ruling regarding the killing of Nawab Akbar Bugti was confirmed by lawyers on both sides.
"It's an injustice and a joke," Suhail Rajput, lawyer for the Bugti family, told media, vowing to appeal.
Bugti was killed in a military operation in 2006, sparking deadly nationwide protests and inflaming a separatist insurgency in resource-rich but impoverished Baluchistan province.
Musharraf, who seized power in a bloodless coup in 1999 and resigned in 2008, is under house arrest in Karachi over numerous criminal charges related to the three cases.
They include treason for imposing emergency rule in 2007, and charges linked to the assassination of opposition leader Benazir Bhutto in a gun and suicide attack that same year.