The news came a day after Egypt jailed three Al Jazeera journalists on charges of aiding the outlawed Islamist Muslim Brotherhood organisation, a ruling condemned around the world as a blow to press freedom.
Al-Baghdadia, Al-Rafidain and Al-Hadath TV stations were all barred from the state-owned Nilesat, which broadcasts across the Middle East and North Africa, the head of Egypt's broadcasting regulator Free Zone said.
The three channels have been off the air in Iraq and Egypt since last week. They often took a pro-Sunni, anti-Iraqi government line that appeals to the country's Sunni minority, although Al-Baghdadiya in particular had investigative programming that attracted a broader segment of the population.
The channels have covered the onslaught by Sunni insurgent group Islamic State in Iraq and the Levant extensively and carried statements from the al Qaeda offshoot.
An official at Free Zone said the decision to block the channels was linked to complaints from Iraq.
The regulator's head, Abdel Moneim Al-Alfy, said: "Al-Baghdadia and Al-Rafidain channels were taken off Nilesat for violating their contracts with the Free Zone authority regarding their content." He did not directly link the decision to complaints from Iraq.
"We have received complaints from the Iraqi government about the channels' contents and are investigating them now."
He said Al-Hadath's permit had expired.
Al-Baghdadia confirmed it was now banned in Iraq and Egypt while Al-Hadath's CEO Ayman Khalid said his channel's closure was temporary and over a financial dispute with Free Zone. Al-Rafidain could not be reached for comment.
Egypt has shut down a number of pro-Islamist channels since the army ousted Islamist President Mohamed Mursi last year.