The court in Balochistan's provincial capital Quetta had charge-sheeted 71-year-old Musharraf last month for the 2006 killing of Bugti.
The judge had ordered that the case would be heard on a daily basis from today onwards.
The court today also expressed anger at Director General Balochistan Naseer Baloch for not submitting Musharraf's medical report and adjourned the hearing till February 25.
Musharraf's counsel had earlier submitted a medical report in the court, requesting the court to allow the former president exemption from appearance due to back pain.
Bugti's son Jamil Akbar had nominated Musharraf, former Prime Minister Shaukat Aziz, former Governor of Balochistan Owais Ahmed Ghani, ex-interior minister Aftab Ahmed Khan Sherpao and others for the murder.
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 fuelled an armed insurgency that began in 2004 in Balochistan.
Musharraf never appeared in the court during the entire legal process which has been in progress since 2009. He was also absent when the charge-sheet was read out in the court. The indictment was the fourth against him.
The ex-army chief is facing a slew of court cases after returning from five years of self-exile in Dubai to contest the general elections in 2013 which he lost.
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 came to power in a bloodless coup in 1999, deposing then-prime minister Nawaz Sharif.
Facing impeachment following elections in 2008, Musharraf resigned as president and went into self-imposed exile in Dubai.
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