The court in Quetta had specifically directed the 71-year-old former President to appear in person but Musharraf, who is in Karachi, did not turn up.
Musharraf's lawyer told reporters that his client was not keeping good health and could not travel to Quetta for the hearing.
"We have also requested the court to hold a separate hearing for this case," Nazeer Ahmed Cheema said.
While Musharraf did not appear for the hearing, two of his guarantors -- former interior minister Aftab Ahmed Khan Sherpao and former home minister Balochistan Shoaib Nowsherwani - appeared before the court today.
Strict security measures were put in by the administration to avert any untoward incident during today's hearing.
Bugti, 79, a high-profile tribal elder and politician from the troubled Balochistan province was killed in August 2006 near Dera Bugti when security forces carried out an operation in the area during Musharraf's tenure.
Bugti's son Jamil Akbar Bugti has nominated Musharraf, former prime minister Shaukat Aziz and others in the murder case of his father.
Since Musharraf returned to Pakistan from self-exile in March last year, he has faced prosecution in four major cases, including one in which he has been indicted on high treason charges and another for his alleged involvement in the murder of former prime minister Benazir Bhutto in 2007.
The former president, who is the first military ruler in Pakistan's history to be tried in court, has rejected all the charges leveled against him.