Islamabad High Court Justice Noorul Haq Qureshi issued the order during the hearing of a petition filed by Haroon Rasheed, son of Lal Masjid's Ghazi Abdul Rasheed, against Musharraf for his involvement in the killing of his father and grandmother.
During the hearing, the Justice said Rasheed's statement should be recorded.
On July 3, 2007, Musharraf had ordered a military crackdown against the mosque for challenging the writ of the state.
The military besieged the mosque for 12 days before assaulting the compound, an attack in which hundreds of students were killed.
The former chief cleric of Lal Masjid was accused of using the mosque loudspeaker to instigate madrassa students to attack the Rangers who were deployed outside the mosque in order to prevent Aziz and his associates at Lal Masjid from continuing their campaign of public intimidation that they had been carrying out since January of that year.
The charges against Aziz also includes kidnapping and abduction of Chinese massage therapists as well as hijacking a children's library in June 2007 as part of his institution's protest against the demolition of seven mosques in the federal capital.
Last year, an anti-terrorism court acquitted Aziz, and 16 other persons in a case on the killing of a Rangers official.
Musharraf had come to power in 1999 by deposing Nawaz Sharif's last government in a military coup.
The 69-year-old former military ruler was arrested shortly after he returned to Pakistan in March to lead his party in the polls.
He is currently being held at his farmhouse on the outskirts of Islamabad and is facing charges in three high-profile cases related to the 2007 assassination of former premier Benazir Bhutto, the killing of Baloch nationalist leader Akbar Bugti in a 2006 military operation and the imposition of emergency in 2007.
The federal government has already decided to initiate high treason case against him for abrogating the constitution and imposing emergency rule in November 2007.