Musharraf's lawyer Akhtar Shah had requested the court to discharge the former president in the case.
After listening to his arguments, the court in Rawalpindi rejected the plea as inadmissible.
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The court also dismissed Shah's request to become a party and a witness in the case, saying he was politically affiliated.
The court has ordered fresh trial in the case that will begin on October 22. It has also summoned three witnesses.
On June 25, the Federal Investigation Agency had submitted a final chargesheet against Musharraf that declared him the "prime accused".
The anti-terrorism court indicted Musharraf on August 20.
The 70-year-old former army chief was arrested by the FIA on April 26 and later granted bail in the case against two surety bonds of Rs 1 million each.
Musharraf is facing serious charges in other cases, including the 2006 Akbar Bugti murder case and for imposing emergency and deposing judges in 2007.
Baloch nationalist leader Bugti was killed in a cave on August 26, 2006 during a military crackdown ordered by Musharraf who was president and army chief at the time.
Yesterday, the Supreme Court rejected Musharraf's petition to move the hearing of the Bugti murder case from Quetta to Islamabad.
Musharraf is currently detained in his farmhouse on the outskirts of Islamabad, guarded by an army of nearly 300 policemen, paramilitary personnel, soldiers, snipers and anti-terrorist officers.
He has been exempted from appearing in the anti-terrorism court because of security concerns.
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