The case was filed on the directions of the Islamabad High Court Justice Noorul Huque Qureshi who was annoyed over non-compliance of its earlier order.
During the hearing of a petition filed by Haroon Rasheed, the son of Lal Masjid's Rasheed, against 70-year-old Musharraf for his involvement in the killing of his father and grandmother, Justice Huque said non-registration of the case despite court order was contempt of court, media reports said.
They said the SHO of Aabpara Police Station Qasim Niazi was made to sit in the court till a case was filed.
Reacting to the verdict, Aasia Ishaque of Musharraf's All Pakistan Muslim League party said he will fight to prove his innocence.
"Musharraf is not going to go away. We were expecting such a case. He will continue to fight politically motivated case and prove his innocence," she told PTI.
The Lal Masjid operation, undertaken by the then Musharraf government in 2007, was meant as a crackdown on the controversial mosque in Islamabad, which ended in a bloody eight-day siege, killing at least 58 Pakistani troops and seminary students.
On Friday, the court had summoned the SHO over non-compliance with the court's orders to look into whether a case can be registered.
On July 12 this year, the same bench had ordered the police to book the former president, and if the Lal Masjid operation was a cognisable offence, a case be registered against Musharraf for the death of cleric and others.
However, the police had refused to register an FIR, saying it would do so after consulting their legal branch.
Musharraf, who returned from his self-imposed exile before the May 11 elections, is currently entangled in a legal web.
He is currently under arrest and his house has been turned into a prison. He is already facing trial for treason, Benezir Bhutto assassination case and also the Akbar Bugti murder case.
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