Fox has also decided to bring forward the production of the film, according to Deadline.
The movie's initial script was written by Adam Cooper and Bill Collage (both Tower Heist), with Steven Zaillian (American Gangster) now having signed up to rewrite it.
The plan is reportedly for Scott to begin work on Exodus immediately after he has completed The Counselor.
Discussing the movie last year, Scott said: "What's interesting to me about Moses isn't the big stuff that everybody knows. It's things like his relationship with Ramesses [II, the pharaoh].
"I honestly wasn't paying attention in school when I was told the story of Moses. Some of the details of his life are extraordinary."
Bale was also recently reported to be close to signing for disaster film Everest.
Photo gallery - Christian Bale's career in pictures: