In one scene, Peter, who sounds like a real bun's rights activist, gangs up with his animal friends and pelts nemesis Tom McGregor with blackberries.
In the new children's movie, a human character named Mr. McGregor (Sam Neill) is allergic to blackberries.
The story pits Peter against villainous farmer Tom McGregor, whose weakness is revealed to be an allergy to blackberries.
Immediately after the movie's release, the group Kids With Food Allergies, a subdivision of the Asthma and Allergy Foundation of America, heard complaints about the scene from parents who condemned the use of allergies as a punchline.
"Additionally, the segment makes light of the seriousness of food allergies and suggests that food allergies are 'made up for attention"'.
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The filmmakers apologized for including the segment "even in a cartoonish, slapstick way".
Critics have found a number of ways to describe Sony Pictures' new adaptation of Beatrix Potter's mischievous yet beloved bunny, "Peter Rabbit".
The scene, which has angered viewers in the USA, where it was opened in cinemas last weekend, shows Tom McGregor, the nephew of Beatrix Potter's notorious Mr McGregor character, being intentionally pelted with blackberries by Peter Rabbit and his friends - resulting in him needing to use life saving emergency medication.
The studio and filmmakers say they regret not being more aware and sensitive to the issue.
Sony Pictures' apology came after the organization Kids With Food Allergies Foundation had slammed Peter Rabbit for the offensive scene.
"KFA believes that food allergy "jokes" are harmful to our community," read the post.
"There is a scene in the movie when someone who has food allergies is intentionally targeted. food allergies are real & my son could DIE if he ate something he's allergic to -It's not something he asked for it's just something he lives with educate yourself #boycottpeterrabbit", wrote user exhausted mom of 3.