Judge Syed Kausar Abbas Zaidi of the anti-terrorism court also accepted a plea from Musharraf's lawyers that he should be exempted from appearing in the court today.
69-year-old Musharraf could not be produced in court for security reasons, officials said.
The judge subsequently adjourned the case till June 1.
Musharraf has also been arrested over the assassination of former premier Benazir Bhutto and the killing of Baloch leader Akbar Bugti in a 2006 military operation.
The former President has been humiliated since he returned to Pakistan from self-exile in March to contest elections.