While Musharraf is already under house arrest and undergoing several trials in Pakistan, Shaukat Aziz has been living abroad since the 2008 elections.
A prosecution lawyer said that the court had issued the non-bailable arrest warrants because of the continued absence of Musharraf and Aziz from hearings.
The former governor of Balochistan, Owais Ghani and former deputy commissioner of Dera Bugti, Samad Lasi were also included in the list of issued arrest warrants.
69-year-old Musharraf is also facing charges over the 2007 assassination of former premier Benazir Bhutto and for detaining dozens of members of the superior judiciary after imposing emergency rule in 2007.
Baloch nationalist leader Bugti was killed in a cave in August 2006 during a military crackdown ordered by Musharraf.
Bugti was the chief of the Jamhoori Watan Party and an influential tribal chief who controlled the gas-rich district of Dera Bugti in Balochistan province.
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