Judge Mohammad Ismaeel Baloch of the anti-terrorism court in Quetta had yesterday heard Musharraf's bail application and reserved his judgement.
During a hearing today, the judge rejected the plea.
Nawabzada Jamil Bugti, the son of Akbar Bugti, has 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 in 2006.
The warrants were issued after Musharraf and the others failed to appear before the judge despite repeated summons.
Meanwhile, the Islamabad High Court granted bail to 69-year-old Musharraf in a case over the detention of dozens of judges after he imposed emergency rule in late 2007.
A two-judge bench directed Musharraf to deposit two security bonds of Rs 500,000 each.
Musharraf's counsel Ilyas Siddiqui told the bench that there was no evidence that his client had ordered the judges' detention and stopped them from performing their duties.
Public Prosecutor Amir Tabish told the court that Musharraf should not be granted bail as he had not proved his innocence in the case.
However, he admitted that there was nothing on record that could be produced as evidence in the case.
The former President was arrested shortly after he returned to Pakistan from self-exile in March.
He has been barred from leaving the country and is being held at his farmhouse outside Islamabad since April 19.
Musharraf is facing charges in several high-profile cases, including the 2007 assassination of former premier Benazir Bhutto, the killing of Bugti and the judges' detention.
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