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The sci-fi thriller, which has been met with tepid reviews, will open in cinemas on Friday without the support of Kassovitz.
The filmmaker, whose previous credits include Gothika and La Haine, called the finished work "pure violence and stupidity" and likened it to a "bad episode of 24".
Kassovitz added: "Fox was sending lawyers who were looking at all the commas and the dots. They made everything difficult from A to Z."
Earlier reports suggested that Babylon A.D.'s running time had been drastically chopped to 90 minutes for its UK release.
The movie, which stars Vin Diesel and Michelle Yeoh, is based on the novel Babylon Babies by Maurice Georges Dantec.
