Musharraf has been accused of murdering Lal Masjid cleric Abdul Rasheed Ghazi during the infamous siege of the mosque.
Rejecting 70-year-old Musharraf's petition, Additional District and Sessions Judge Wajid Ali Khan has summoned the former president on May 3.
During the hearing, Musharraf's counsel presented his arguments saying that the former army chief faced death threats, adding that he was targeted in an attack two days earlier as a result of which he could not appear in court.
The court granted Musharraf exemption from appearance for today's hearing and adjourned the case to three months.
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But the former president's request seeking permanent exemption from attending the case's hearings was dismissed.
Rasheed was killed during the storming of the Lal Masjid, a government crackdown on the controversial pro-Taliban mosque in Islamabad.
The operation had ended in a deadly eight-day siege killing at least 58 Pakistani troops and seminary students.
The operation, ordered by Musharraf, followed a week-long standoff between the mosque's supporters and security forces.
On September 2, a case was registered in the Islamabad High Court (IHC) against Musharraf for the murder of the former cleric and his mother during the Lal Masjid operation.
In the application, Haroon had referred to about 20 pages of the Lal Masjid Commission report, which hold the former president responsible for the operation.
Since his return to Pakistan from self-exile in March last year, Musharraf has faced prosecution in four major cases, including for his alleged involvement in the murder of former prime minister Benazir Bhutto in 2007 and the killing of Baloch nationalist leader Akbar Bugti in 2006.