Judge Mohammad Ismaeel Baloch of the anti-terrorism court in Quetta yesterday heard the bail application filed by Musharraf's counsel Mohammad Ilyas and reserved his judgment.
During a hearing today, the judge rejected the bail application.
Bugti was killed in a cave in August 2006 during a military crackdown ordered by Musharraf.
Nawabzada Jamil Bugti, the son of Akbar Bugti, had named Musharraf, former premier Shaukat Aziz, former Interior Minister Aftab Ahmed Khan Sherpao, former Balochistan Governor Owais Ghani and local official Abdul Samad Lasi for being responsible for his father's murder.
The court issued the warrants after Musharraf and the others failed to appear before the judge despite repeated summons.
The 69-year-old former President was arrested shortly after he returned to Pakistan from self-exile in March to contest the May 11 general elections.
He is facing charges in several high-profile cases, including the 2007 assassination of former premier Benazir Bhutto and the detention of dozens of judges during the 2007 emergency.
The former army chief is currently being held in his farmhouse in Islamabad, which has been declared a "sub-jail".
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