The ordinance amended the Provisional Constitutional Order (PCO) Musharraf had issued on November 3 in his capacity as army chief to suspend the Constitution and key fundamental rights like the freedom of expression.
Under the new amendment, no one will be allowed to challenge the emergency or the PCO in a court, Dawn News channel reported.
The amendment said all decisions made by the government during the emergency would also be valid and could not be questioned in a court.
The move came as the Supreme Court was hearing two petitions against the emergency. The court is expected to rule on the matter on Thursday.
Musharraf had on November 15 issued another order to amend the PCO to give the President the power to revoke the emergency.
The emergency and PCO were issued by Musharraf as army chief and could have been revoked by him only in that capacity, legal experts said.