The Anti-Terrorism Court in Quetta issued the warrants against Mumtaz Ahmad and Nazeer Ahmad after the 70-year-old former president failed to appear in court yesterday.
The hearing of the case was adjourned to April 7.
Baloch nationalist leader Akbar Khan Bugti was killed in a cave on August 26, 2006 during a military crackdown ordered by Musharraf, who was then president and army chief.
Bugti had led an armed campaign to press for provincial autonomy and a greater share of profits from Balochistan's natural resources. His death triggered angry protests across the country.