The head of the censorship board said these included the film's depiction of Jews as having built the Pyramids, and that an earthquake, not a miracle by Moses, caused the Red Sea to part.
Exodus: Gods and Kings stars Christian Bale as Moses.
There have also been reports that the film is banned in Morocco.
Although the state-run Moroccan Cinema Centre (CCM) had given the film the green light, Moroccan business website Medias24.com said that officials had decided to ban the movie from being screened the day before its premiere.
According to the book of Exodus, Jewish slaves were led to freedom by Moses after God inflicted a series of plagues on Egypt.
The Pyramids are believed to have been built about 1,000 years before the story of the Exodus.
The Biblical story tells how the Red Sea was parted by a miracle performed by God through Moses, allowing the Jewish people to escape from the pursuing Egyptian army.
Exodus: Gods and Kings, which cost a reported $140m (£89m) to make, took $24.5m on its debut weekend.
Mixed reviews
The Biblical epic overtook the third instalment of The Hunger Games, following three weeks at number one. However, it has had mixed reviews.
Time called it a "cinematically uninspired retelling of the Moses story", Vulture said it was "as uneven as Ridley Scott's career", while the New York Times described it as "both woefully insufficient and much too much".
The film's opening fell well short of other modern Biblical films, including Darren Aronofsky's Noah which took $43.7m on its opening weekend in March and 2004's The Passion of the Christ, which took $83.3m.
