The scene in question portrays rabbit arch enemy Mr McGregor, who is allergic to blackberries, being pelted with the berries by a gang of bunnies. He ultimately has an allergic reaction that requires the use of an epipen.
The animated movie, based on the beloved animal characters created by British author Beatrix Potter, began its worldwide roll out last week.
Groups representing allergy sufferers say the scene made light of a serious and dangerous health problem. The criticism prompted calls on social media to boycott the film, under the hashtag #boycottpeterrabbit.
"Food allergies are a serious issue," Sony Pictures and the "Peter Rabbit" filmmakers said in a statement.
"Our film should not have made light of Peter Rabbit's archnemesis, Mr McGregor, being allergic to blackberries, even in a cartoonish slapstick way. We sincerely regret not being more aware and sensitive to this issue, and we truly apologise."
The Kids With Food Allergies Foundation, a division of the Asthma and Allergy Foundation of America, last week sent a letter to Sony and the filmmakers raising concerns about the scene.
In a related Facebook post, the group said "making light of this condition hurts our members because it encourages the public not to take the risk of allergic reactions seriously, and this cavalier attitude may make them act in ways that could put an allergic person in danger."
"Peter Rabbit," starring voice actors James Corden and Domhnall Gleeson, took $25 million USD at the North American box office on its opening weekend. It opens in Australia 22 March 2018.