A petition calling on Sony Pictures to apologise also attracted thousands of signatures.
In Peter Rabbit, released next month, the rabbits' arch nemesis Mr McGregor has died and his nephew Tom takes charge of the vegetable patch with a renewed vigour and disdain for the "vermin".
Sony has now issued a statement apologising for the scene, saying that "we sincerely regret not being more aware and sensitive to this issue".
"Additionally, the segment makes light of the seriousness of food allergies and suggests that food allergies are "made up for attention'".
The offending scene is shown in a film adaptation of the Beatrix Potter book Peter Rabbit, which was released in USA cinemas this weekend.
The online petition was started by Globalaai, an organisation that describes itself as "a worldwide allergy and anaphylaxis movement for positive change of social awareness and safety".
The new Peter Rabbit movie is facing the wrath of food allergy advocacy groups after one of the film's characters is attacked with their allergen.
Supporters argue the scene is "heartbreakingly disrespectful" to families who have lost loved ones to anaphylaxis, a serious allergic reaction causing death.
"KFA believes that food allergy "jokes" are harmful to our community", the foundation wrote on Facebook. "To spread a message that condones such victimising and unsafe behaviour amongst children is grossly offensive to worldwide viewers especially those who live with severe allergic disease".
The post encouraged parents to discuss the scene with their kids prior to taking them to the movie and said "making light" of allergic reactions could be at the cost of another person's life.
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