The decision by the administrative court was expected amid an escalating campaign by the government against the TV station and other media it considers sympathetic to ousted President Mohammed Morsi, who hails from the Muslim Brotherhood group. Al-Jazeera officials were not immediately available for comment.
Last week, three government ministries issued a statement calling the broadcasts of Al-Jazeera Mubasher Misr a "national threat" and accusing it of spreading rumors. They said that the station would soon be ordered closed.
The ministers also said the channel used satellite transmission without a license and spread "rumors and claims which are harmful to Egyptian national security and threaten the country's unity."
The station extensively covered Brotherhood protests following the July 3 military coup that ousted Morsi after millions took to the streets demanding he step down. In recent weeks, it began broadcasting recorded messages from Brotherhood members who are wanted by authorities and are hiding.
Egyptian officials and media say the station is biased toward the Brotherhood, a charge Al-Jazeera denies.
The third station, Ahrar 25, is affiliated with Egypt's Muslim Brotherhood, and sprung up after authorities shut down their licensed Misr 25 television channel and four Islamic TV networks sympathetic to the deposed president on the day he was ousted.
Al-Jazeera's local offices were raided after Morsi was deposed, and 28 staffers were detained. They were later released.
Officials have earlier said that the Al-Jazeera affiliate continued to broadcast live from protests using via a stolen van owned by Egyptian state TV.
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