Local media reported that about 150 protesters in Islamabad had been arrested by police, who used water cannon, rubber bullets and tear gas.
A statement issued later on Saturday by PEMRA stated TV channels to show sensitivity regarding the matter and stop live coverage of the operation.
The protests, which spread on Saturday to several other cities in Pakistan, have left about 200 injured, including dozens of police officers.
The Pakistan Electronic Media Regulatory Authority took private television stations off the air.More news: Nebraska Approves Keystone XL Pipeline -- But Sets a New Route
Pakistan's Geo News reported that in Islamabad, protesters are firing teargas shells at the security forces. The people give elevated status and respect to the religious scholars in our society but the very conduct of the religious protestors in Islamabad only undermined the religious community. Key social media sites like Facebook, Twitter and YouTube were also blocked.
Earlier, the Chief of Army Staff (COAS) General Qamar Javed Bajwa telephoned Prime Minister Shahid Khaqan Abbasi and discussed the ongoing situation regarding the crackdown on protesters in Islamabad.
Despite a swift reversal, protesters still demand that Pakistan's law minister resign.
Pakistan Interior Minister Ahsan Iqbal had given protesters around Islamabad until last Thursday to disperse, but they continued their demonstration.
Dawn said nearly 8,000 security personnel started operation at 7 am after last deadline ended on Saturday.More news: Kremlin comments on senator's detention in France
"The administration is taking action under court order but still we are open for talks with them", he said, referring to the protesters.
A senior government official speaking on condition of anonymity, due to restrictions on speaking to the media, told Anadolu Agency that the security forces had been asked not to take on the violent protesters pending further orders.
The protesters had occupied the Faizabad Bridge which connects Rawalpindi and Islamabad through the Islamabad Expressway and Murree Road, both of which are the busiest roads in the twin cities.
In Lahore, an unruly mob torched a vehicle and damaged others with stoning and staged sit-ins at four key areas in the city.More news: CBS And Dish Network Reach Deal, Ending Blackout