Qatar, Bahrain and the United Arab Emirates told Hollywood giant Paramount last week that the film, starring Russell Crowe, will not be released in their countries. Egypt, Jordan and Kuwait are expected to follow suit.
The movie was due to open in Egypt on March 26 and the UAE on March 27, just before the movie comes out in the United States and a swath of other countries.
But a Paramount spokesman said: "The censors for Qatar, Bahrain, and the UAE officially confirmed the film will not release in their countries.
Egypt's top Islamic body, the Al-Azhar institute, said last week that the big budget film violated Islam by portraying a prophet and should not be screened in the country.
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Having an actor play a prophet "contradicts the stature of prophets and messengers... And antagonizes the faithful," it said in a statement. Muslims believe Jesus was a prophet and was not crucified.
Egypt has censored other movies in the past, including "The Da Vinci Code", after protests from the Orthodox Coptic Church. But it did allow the screening of Mel Gibson's "The Passion of Christ", which depicts Jesus being crucified.
Last month Paramount announced that they would add an explanatory message to future marketing materials for the movie by acclaimed filmmaker Darren Aronofsky.
It issued a joint statement with the National Religious Broadcasters (NRB) body, announcing the move "to help audiences better understand that the feature film is a dramatization of the major scriptural themes and not a line-by-line retelling of the Bible story.