The piece, headlined 'Hot wings', took a humorous view of the bird cull, with captions such as "Who ordered a flame-grilled?".
Since the article appeared in a February issue of the lads' mag, the RSPCA, People for the Ethical Treatment of Animals, and Compassion in World Farming have all received letters from readers objecting to the story. All have since lodged their own complaints with Emap.
In a letter to Emap Consumer Media's chief executive Paul Keenan, RSPCA International said such articles trivialise suffering and "may even lead some young people to commit acts of cruelty".
The US arm of Peta described the pictures as "horrifying" and Zoo Weekly's treatment of them as "sad and shameful". Its correspondent Janice Krish said animal abuse and insensitivity to cruelty is a "symptom of a pathological mentality".
None of the charities have had a response. An Emap spokeswoman said: "It was a valid news story, but we apologise if the Zoo's interpretation caused offence."