The petition, filed in the Islamabad High Court, challenged Justice Riaz Ahmad Khan's decision to reject three earlier pleas by Musharraf against the special court.
"We have filed an intra-court appeal against the December 23 order of the court, which had dismissed our previous applications. We have now filed it before a larger bench," Mohammad Ali Saif, a key member of Musharraf's legal team, told PTI.
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Musharraf alleged the formation of the special court was a "combined conspiracy" by Prime Minister Nawaz Sharif and former Chief Justice Iftikhar Chaudhry and hence, it should not be allowed to function.
The special court was to have begun the trial on December 24 but the 70-year-old former army chief did not attend the first hearing after explosives were found on the route he was to take from his home to the court.
In a separate development, the Islamabad High Court gave time till January 3 to a man named Akhtar Shah to submit documents related to his application asking for Musharraf to be excused from appearing in court for the treason case.
Asked if Shah's petition was part of the strategy adopted by Musharraf, Saif said, "We don't have any relation with it. We have only filed two petitions. One, the intra-court appeal and the other one in the special court asking it not to hear the matter as we don't recognise it."
Musharraf has been accused of treason for imposing emergency and suspending the Constitution in November 2007. He is the first general to face such charges and could be given life imprisonment or the death penalty if he is convicted.
While challenging the authority of the special court, Musharraf said he had imposed emergency in his capacity as the army chief and a military court alone could examine his actions.
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