Justice Khwaja Imtiaz Ahmad of the Rawalpindi bench of Lahore high court issued the order against Musharraf, former chief minister Pervaiz Elahi, ex-interior minister Hamid Nawaz Khan and former interior ministry official Javed Iqbal Cheema.
The court's move came in response to a petition filed by Chaudhry Mohammad Aslam, Bhutto's former protocol officer who was injured when she was assassinated by a suicide bomber in December 2007.
Aslam has asked the court to direct the authorities to register a first information report against Musharraf and some of his close aides for their alleged involvement in the killing.
The court order came after Musharraf and the three other persons did not file representations in the court despite repeated notices issued to them.
During the last hearing, the court had also warned that it would go ahead with ex-parte proceedings against three more persons named in Aslam's petition - Parliamentary Affairs Minister Babar Awan, former Intelligence Bureau chief Ijaz Shah and former Rawalpindi district administration chief Irfan Elahi.