The film relates how Moses helped Israelite slaves flee persecution in Egypt under the Pharaoh Ramses by parting the Red Sea to let them cross safely.
Culture Minister Gaber Asfour told AFP that Ridley Scott's blockbuster was rife with mistakes, including an apparent claim that "Moses and the Jews built the pyramids".
"This totally contradicts proven historical facts," Asfour said.
"It is a Zionist film," he said. "It gives a Zionist view of history and contains historical inaccuracies and that's why we have decided to ban it."
The ban was decided by a committee comprising the head of the supreme council for culture, Mohammed Afifi, the head of the censorship committee and two history professors, said Asfour.
Afifi said he took issue with the scene showing the parting of the Red Sea in which Moses -- a prophet revered by Jews, Christians and Muslims alike -- is seen holding a "sword" like a warrior, instead of a "stick".
Furthermore, he said, the parting of the Red Sea is explained in the movie as a "tidal phenomenon" rather than a divine miracle.
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Morocco has also banned the film, despite it already having been approved by the state-run Moroccan Cinema Centre, media reported on Thursday, quoting theatre managers.
Hassan Belkady, who runs Cinema Rif in Casablanca, told media24 news website that he had been threatened with the closure of his business if he ignored the ban.
"They phoned and threatened they would shut down the theatre if I did not take the film off the schedule," Belkady said.
In March, Al-Azhar, Egypt's top Islamic body, banned the screening of "Noah", another Hollywood biblical epic starring Russell Crowe, saying it violated Islam by portraying a prophet.
The film triggered controversy in the United States where some Christian institutions criticising Crowe's reportedly unconventional portrayal of Noah.
"Exodus" has also sparked unkind reviews and upset some Christian groups, with critics saying Scott took too many liberties with the Bible and cast Western actors in Middle East roles.
Egypt has censored other movies in the past, including the blockbuster "The Da Vinci Code" after protests from the Orthodox Coptic Church.
But it did allow the screening of Mel Gibson's "The Passion of The Christ", which depicts Jesus being crucified.
Muslims believe Jesus was a prophet and was not crucified.