The case was formally lodged by the state-run Radio and Television Union, which is the sole owner of broadcast signals in Egypt.
The group has been in the news since it distributed footage of protesters tearing up posters of Hosni Mubarak, the Egyptian president.
Nader Gohar, CNC's owner, told Al Jazeera his firm did have licences with the union but, in common with other media firms, he was unable to renew them after the government announced it would review its policy on issuing permits.
He said: "It will be the same situation for the six other companies doing the same business in Cairo."
When asked if he believed he had been targeted by the Egyptian authorities, Gohar replied: "Maybe, we are the biggest company in here and we have good relations with foreign media."
Gohar said the ruling means his firm could be out of business for between six months to a year.
The Radio and Television Union brought the complaint against CNC on April 8, 2008 - two days after Al Jazeera broadcast coverage of large anti-government protests in the Nile Delta.
Human Rights Watch, the international rights group, accused the Egyptian authorities of enforcing media licensing laws to punish the company for distributing anti-government material.