The court in provincial capital Quetta charge-sheeted the 71-year-old leader and adjourned the hearing till February 4.
The judge said that the case would be heard on a daily basis from February 4 onward.
Bugti, former chief minister of Balochistan and head of his tribe, was killed in 2006 in a military operation ordered by Musharraf who was president and army chief at the time.
His killing sparked nationwide protests and further fulled an armed insurgency that began in 2004 in Balochistan.
Two co-accused - Musharraf's interior minister Aftab Khan Sherpao and ex-provincial home minister Shoaib Nusherwan - were also indicted for their alleged role in murder of the Baloch tribal leader.
Musharraf never appeared in the court during the entire legal process which has been in progress since 2009. This led to his indictment.
He was absent when the charge-sheet was read out in the court.
Earlier, Musharraf's counsel submitted a medical report in the court, requesting court to allow the former president exemption from appearance.
He said Musharraf was suffering back pain.The court said the exemption would be granted only after a medical board examine Musharraf and make independent judgment about his health.
Musharraf is already facing murder charges in the case of former premier Benazir Bhutto who was assassinated in 2007. He is on bail in the case.
Musharraf is facing a slew of court cases including one for high treason after returning in 2013 from five years of self-exile.


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