Earlier in the day, security forces fired tear gas and rubber bullets as the demonstrators burned police vehicles around the site of the sit-in.
A statement issued later on Saturday by PEMRA stated TV channels to show sensitivity regarding the matter and stop live coverage of the operation.
At least one person was killed and over 200 injured after police moved in to break "blasphemy" protests..
Private television channels in Pakistan were taken off the air by the Pakistan Electronic Media Regulatory Authority, according to a message slate that replaced the channels' programming.
Pakistan's Geo News quoted police as saying that the suffered a deadly blow to the head in I-8/4 sector as protesters pelted stones at security officials during the operation at Faizabad interchange.
A protester walks near burning tents during clashes with police at Faizabad junction in Islamabad, Pakistan November 25, 2017. There are also reports of social media blackout in some parts of Pakistan.
Ahsan Iqbal said that protesters had been holding Twin Cities of Islamabad and Rawalpindi hostage for last 20 days, adding that few elements were misleading innocent minds.More news: Longtime country singer, songwriter Mel Tillis dies
The interior minister said the protesters had also "contacted India", according to a report in the newspaper.
The newspaper says 150 protesters were arrested as the operation kicked off.
Army chief General Qamar Javed Bajwa talked to Prime Minister Shahid Khaqan Abbasi and asked him for a peaceful solution to the problem.
The protesters, who before Saturday numbered some 2,000 people, are demanding that Pakistan's law minister Zahid Hamid resign over a hastily-abandoned amendment to the oath that election candidates must swear.
"Patients dying for want of access to hospitals, traders crying for lack of business activity, students are being deprived from their right to education and [the] right of free movement of nearly six million people of [the] twin cities [is being] usurped", he said.
The sincerity of the government to handle the situation amicably could also be gauged from the fact that despite clear instructions from the courts to use any mean to disperse the protestors, it demonstrated restraint and firstly opted for the dialogue.