A divisional bench of the Balochistan High Court passed the order during hearing of review petition challenging acquittal of the 73-year-old former president by an Anti- Terrorism Court in the case, Dawn reported.
Justice Jamal Mandokhail and Justice Zaheeruddin Kakar heard a review petition filed by Nawabzada Jamil Bugti, the son of Akbar Bugti.
The counsel of Musharraf, Akhtar Shah pleaded to the court that although his client respects the court, he cannot appear before the court due to "security reasons".
The court ordered that the administration should ensure adequate security to Musharraf while he appears in court.
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Pakistan government had allowed Musharraf to go abroad in March this year for medical treatment.
Baloch leader Nawab Akbar Bugti was killed in an operation in Balochistan's rugged mountains of Taratani in Kohlu district on August 26, 2006.
Bugti had led an armed campaign to press for provincial autonomy and a greater share of profits from Balochistan's natural resources.
The death of the Baloch chieftain had sparked angry protests in parts of the country.
He was not allowed to leave the country until government allowed him in March this year to go abroad for treatment following orders by the Supreme Court.
Musharraf has been facing a slew of cases, including the high treason trial since 2013 and he was barred from leaving the country in 2014 by the government.
Musharraf seized power in a bloodless coup in 1999, deposing the then Prime Minister Nawaz Sharif.