Morocco is scheduled to host the tournament from January 17 to February 8 next year, but that could be delayed.
Over 3,500 people have died from the virus, which began in west Africa and is ongoing.
It could lead to the Cup of Nations being postponed, with a bid to delay it already reportedly lodged with organisers.
According to the BBC, a statement from the Morocco health ministry said they want "to avoid events which involved those countries affected by the Ebola virus".
Ebola has already affected qualifying for the event, with several matches relocated.
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