Chief Justice Iftikhar Chaudhry directed the country's five High Courts to nominate a judge each by tomorrow for the three-member special court that will try the 70-year-old Musharraf.
He will choose the three judges who will hear the treason case, a charge that could entail the death penalty or life imprisonment.
Chaudhry acted after the Law Ministry sent a letter to the apex court Registrar's Office seeking the formation of a special court to try the former army chief for high treason.
Musharraf's spokesperson has described the government's decision to initiate the case against him as a "vicious attempt to undermine the Pakistan military".
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The military has ruled Pakistan for about half of its 66-year history and no ruler or top military commander has ever faced criminal prosecution.
Earlier in the day, the Sindh High Court adjourned the hearing of Musharraf's petition for removing his name from the Interior Ministry's Exit Control List till November 22.
In his plea, Musharraf said he wants to go to Dubai to meet his ailing mother. Persons included in the Exit Control List are barred from travelling out of Pakistan.
Interior Minister Chaudhry Nisar Ali Khan yesterday said the government decided to initiate treason proceedings against Musharraf under Article 6 of the Constitution in line with a judgement of the Supreme Court and a report submitted by an inquiry committee of the Federal Investigation Agency.
The former President would have to be held accountable for violating the Constitution, Khan said.