The magistrate told the police that remand can only be given in the presence of the suspect and ordered them to present 70-year-old former military ruler before the court.
Musharraf, who had secured his release yesterday following bail being granted in the Akbar Bugti murder case, found himself under arrest again last night on charges of murdering the 'prayer leader' of Lal Masjid, Abdul Rasheed during the infamous 2007 operation.
Police had earlier refused a request by leaders of Lal Masjid to name the former military ruler as a suspect in the case of a military raid in 2007 which saw dozens killed including one of the administrators.
On orders from the Islamabad High Court, a case was finally registered against Musharraf on September 2 charging him with the murder of Abdul Rashid and his mother during the Lal Masjid operation, paving way for recent arrest.
The case was filed after Haroon Rasheed, the son of the cleric, submitted an application at the Aabpara police station for the registration of an FIR against the former president.
In the application, Rasheed had referred to about 20 pages of the Lal Masjid Commission report, which held the former president responsible for the operation.
Musharraf took power in a 1999 coup and ruled as President until he resigned.
On October 9, Musharraf was granted bail by a three-judge bench of the Supreme Court in the Bugti murder case on account of insufficient evidence against the accused.
He had already received bail in the Benazir Bhutto assassination case and the judges' detention case. The former military strongman is currently being held at his farmhouse on the outskirts of Islamabad, guarded by nearly 300 security personnel, including soldiers and snipers.
Musharraf took power in a 1999 coup and ruled as President until he resigned when he was threatened with impeachment in 2008. He then went into self-imposed exile and returned to Pakistan in March in a bid to resurrect his political career.