The original instruction gave PEMRA powers to seal broadcast premises or confiscate broadcasters' equipment, as well as suspend their licences should they break a code of conduct.
Although Musharraf has granted unprecedented media freedoms in Pakistan since taking power in a 1999 coup, he has lately complained of bias in the coverage of the suspension of Iftikhar Chaudhry, Pakistan's chief justice.
Several private broadcasters have recently criticised the army's support for Musharraf, who is also Pakistan's military chief.
A series of public demonstrations, mainly led by journalists, were held after Musharraf's ordinance was issued.
The implementation of the decree had already been suspended by Shaukat Aziz, Pakistan's prime minister, after a spat between journalists and government officials in parliament on Wednesday.
Musharraf is facing the biggest crisis of his eight years in power since suspending Chaudhry in March.
Political violence in Karachi on May 12 left more than 40 people dead.