The announcement came a day after the airline said it had decided to lift a suspension of flights to Syria, put in place because of fighting around Damascus International Airport.
The airport is close to Sunni Muslim towns and suburbs that have been at the forefront of the revolt against Syrian President Bashar al-Assad.
The Osama Bin Zeid Brigades, one of several Islamist rebel units operating around the capital, described the 20-km (12 mile) airport road as a "battleground territory" and warned civilians not to use it in a statement.
"Egyptian authorities told Flight 721 to go back to Cairo, based on information received from Damascus," the EgyptAir official said.
Other airlines told Reuters their flights were still suspended, citing concerns by local staff that the road was still unsafe.
(Writing by Khaled Yacoub Oweis; Editing by Andrew Heavens)
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