A scene in the film shows a character who suffers a blackberry allergy being pelted with them by a gang of bunnies.
In a joint statement, Sony Pictures and the filmmakers said they "should not have made light" of the issue.
Campaigners condemned the scene and some Twitter users adopted the hashtag #boycottpeterrabbit.
The charity Kids with Food Allergies Foundation said in a Facebook post "food allergy 'jokes' are harmful to our community".
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BBC NEWS