Pervez Musharraf, Pakistan's president, has accused some television networks of broadcasting unbalanced reports against his rule.
Government attempts to remove Chaudhry from his position have sparked a wide campaign by his supporters and opposition parties against Musharraf.
"They have been disrupting our transmissions and making things difficult for us because of our coverage"
Nasir Baig Chugtai, News Director,
The campaign is the largest challenge to Musharraf's authority since he came to power in 1999.
"The PEMRA can [now] confiscate transmission equipment or withdraw the licence of any broadcaster who violates its rules," said Mansoor Ahmed, the secretary of the ministry of law.
Two private television stations said their transmissions had been disrupted on Monday.
Syed Talat Hussain, news director at Aaj channel, said before the new ruling: "They have been disrupting our transmissions and making things difficult for us because of our coverage."
Nasir Baig Chugtai, news director at Geo channel, said: "There was a smooth flow of information which I think has hurt someone and that's why they're taking such actions."
PEMRA has denied interfering with transmissions.
In response to the tougher controls about 100 journalists, opposition party members and pro-democracy campaigners marched from Geo's Islamabad office to the federal parliament building on Monday evening.
Shamim-ur-Rehman, president of the Karachi Union of Journalists, said in a speech: "They want to suppress our voice, but this will not happen,"
Mohsin Raza, director of news for the ARY One World channel, said suspension threatened advertising revenues.
He said: "This will let the budding electronic media starve and thousands of people's jobs will be at risk."