The court also tasked the Federal Investigation Agency (FIA) to complete the investigation by December 17 and report it.
It also rejected a plea by Musharraf's lawyer, Farogh Nasim, to include investigators from army-run intelligence agencies in the team tasked to carry out the fresh probe.
After sweeping to power in 2013, the ruling Pakistan Muslim League-Nawaz (PML-N) constituted a three-member special court to try Musharraf for allegedly subverting the Constitution in November 2007.
Under the 1973 constitution, abrogation of the constitution will be an act of high treason, liable to death under Pakistan's treason laws.
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State prosecutor Akram Sheikh opposed the reinvestigation and said that nothing changed materially as the same government was in the office which launched the treason case.
He said that Musharraf failed to cooperate with the FIA during the process of investigation, despite several notices given to him.
"The federal government will file a review petition against Islamabad High Court's verdict in this case," Sheikh said.
He grabbed power in 1999 by deposing then prime minister Nawaz Sharif and ruled till 2008 when he was forced to resign.
Musharraf lives in Karachi with his daughter. He is not allowed to leave the country under an order by the court.