The court in provincial capital Quetta charge-sheeted the 71-year-old ex-military ruler in Nawaz Akbar Khan Bugti's murder case 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.
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 the murder of the Baloch tribal leader.
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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 the court to allow the former president exemption from appearance.
The court said the exemption would be granted only after a medical board has examined Musharraf and made an independent judgment about his health.
Musharraf is facing a slew of court cases after returning from five years of self-exile in Dubai to take part in general elections in 2013.
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 was also indicted in a high treason case in March last year for suspending, subverting and abrogating the Constitution and imposing an emergency in the country in November 2007, the first army chief to face such a prosecution. He has also been charged in the judges' detention case.
Musharraf, facing impeachment following elections in 2008, resigned as president and went into self-imposed exile in Dubai.