Chief Justice Qazi Faez Isa of the Balochistan High Court dismissed an application submitted on behalf of the former president. (Agencies)
Isa directed the government to ensure 70-year-old Musharraf's safety during a hearing in the court on May 19.
The Chief Justice said Musharraf who is in Karachi can seek exemption from appearing in person in the court after he has heard the charges against him in the murder case.
Bugti, a powerful tribal leader, was killed during a security operation in Dera Bugti by security forces.
Anti-Terrorism Court (ATC) Quetta Judge Justice Anwar Kasi had dismissed Musharraf's application for exemption from appearing in person, after which he had approached the Balochistan High Court.
ATC Quetta had issued five orders to Musharraf to appear in the case but he is yet to make an appearance.
Musharraf has been named as an accused in the murder of the former Balochistan chief minister and governor.
The charge sheet in the case has been submitted but a trial is yet to begin as Musharraf has never appeared in court for indictment.
"If the charges were framed in the presence of the client then he would be at liberty to file application for exemption at a later stage," the court said.
Musharraf's counsel Muhammad Ilyas Siddiqui stated that the former president anticipates a threat to his life from different organisations and that the trial judge should allow his exemption from personal appearance.
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.
Musharraf was indicted on March 31 in the treason trial for suspending, subverting and abrogating the Constitution, imposing an emergency in the country in November 2007 and detaining judges of the superior courts.
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.
Chief Justice Qazi Faez Isa of the Balochistan High Court dismissed an application submitted on behalf of the former president.