The scene in question shows a character with an allergy to blackberries being hit with the fruit by a group of rabbits.
The film was released in the U.S. last week and according to America's Kids With Food Allergies Foundation (KFA), it includes a scene where a character is intentionally attacked with his allergen, which leads to anaphylaxis.
"Given that this movie is aimed at children, to see a character being intentionally attacked with the allergen that they're allergic to has been really disturbing worldwide, not only for the allergy community but also for parents", Globalaai founder Dr Pooja Newman said.
He inhales one of the berries, and then has to stab himself with an epipen to stave off an anaphylactic episode.
Sony Pictures said in a joint statement with the filmmakers that "food allergies are a serious issue" and the film "should not have made light" of a character being allergic to blackberries "even in a cartoonish, slapstick way".
In conclusion, the organization offered to educate Sony and the cast about food allergy "realities" and the "gravity of the disease".
The film was released in United States cinemas this weekend and is an adaptation of Beatrix Potter's book Peter Rabbit.
The studio and filmmakers say they regret not being more aware and sensitive to the issue.
"This isn't the first time that Sony Pictures Animation has used food allergies as a punchline in the plot of a kids" movie", the letter said.
"During a reaction, patients require the life-saving drug epinephrine and must go to the nearest hospital for follow-up treatment", it said.
"The very real fear and anxiety that people experience during an allergic reaction (often referred to as an impending sense of doom) is a serious matter".
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.