The studio rejected a screenplay by Basic Instinct writer Joe Eszterhas, leaving the project in limbo, according to The Hollywood Reporter.
However, the news follows reports of a bitter feud between Gibson and Eszterhas, in which the latter accused the Lethal Weapon actor of using offensive, sexist and racist language.
He also alleged that Gibson's Maccabee project is simply a means to diffuse accusations of anti-semitism. Gibson hit back at Eszterhas in a nine-page letter obtained by Deadline, dismissing his claims as "utter fabrications".
"I would have thought that a man of principle, as you purport to be, would have withdrawn from the project regardless of the money if you truly believed me to be the person you describe in your letter. I guess you only had a problem with me after Warner Brothers rejected your script," Gibson wrote.
"Contrary to your assertion that I was only developing Maccabees to burnish my tarnished reputation, I have been working on this project for over 10 years and it was publicly announced 8 years ago.
"I absolutely want to make this movie; it's just that neither Warner Brothers nor I want to make this movie based on your script."
Gibson will produce the movie through his Icon Productions. The Apocalypto helmer was reportedly waiting to read a draft of the script before deciding whether to direct or star in the film.
The untitled drama will tell the story of the leader of the Jewish revolt against Greek-Syrian armies in the second century BC. It was allegedly first discussed between Gibson and Warner Bros after his 2006 Malibu arrest, when he was accused of insulting a Jewish police officer.
Gibson completed a court-ordered anger management programme earlier this year following charges of battery against ex-girlfriend Oksana Grigorieva.
Warner is currently deciding whether to order another draft of the screenplay or scrap the project altogether.