The project was to team Bale with director James Mangold on the thriller.
Fox has put the film, its adaptation of the John D MacDonald mystery-adventure book series that was to have, on back burner, said The Hollywood Reporter.
Bale, 41, who was to have starred in the project as a freewheeling ex-soldier living on a house boat and acting as a self-proclaimed "salvage consultant," tore his anterior cruciate ligament.
It will prevent him from filming "Goodbye", which was to have been a physically intensive shoot. The climax, for example, was an intense action sequence on boats.
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James Mangold was set to direct the thriller, which also had Peter Dinklage and Nicola Peltz on board to co-star. The planned May start of production in Florida and Puerto Rico has been deep-sixed.
The "Deep Blue Goodbye" project has been in development since the late 1990s, with Oliver Stone and Paul Greengrass among those slated to direct.
Leonardo DiCaprio was at one point set to star and is one of the producers. With years of development invested, Fox is not likely to bid adieu to Goodbye for good.