District and Session Judge Kamran Busharat Mufti rejected Musharraf's plea to grant him exemption from appearing in the court and issued the arrest warrant against the former president.
The court set the next hearing on July 24.
Judge Kamran Basharat Mufti had yesterday reserved the verdict over giving Musharraf exemption from appearance in the court.
71-year-old Musharraf currently lives in Karachi in the house of his daughter and has been dodging courts over ill-health.
The ex-army chief, who ruled from 1999 to 2008, is facing a slew of court cases after returning from five years of self-exile in Dubai to contest the general elections in 2013 which he lost.
Musharraf is already facing murder charges in the killing of Baloch leader Nawab Akbar Bugti in 2006 and in the case of former premier Benazir Bhutto, who was assassinated in 2007.
He has been barred by the Supreme Court from leaving the country.
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