Grand Imam Ahmed al-Tayeb of Al-Azhar had demanded that the authorities ban "With Islam" presented by controversial intellectual reformer Islam Behairy and aired by private channel Al Qahera Wel Nass.
Al-Azhar accuses Behairy of "regularly attacking Islamic law".
Although Al-Azhar advocates tolerance and moderate Islam in conferences, it also routinely asks for programmes and shows in which secular Egyptians criticise current Islamic practices or heritage to be banned.
Behairy has infuriated Al-Azhar's traditional clergy in the past with attacks on canonical religious books and some of Sunni Islam's most important scholars.
Behairy can still appeal against the ban on his broadcasts.
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