Cosmic Cavallaro's sculpture, titled 'My Sweet Lord', caused outrage among Christian groups - who were especially offended because the statue was being aired over the Easter period.
Catholic League head Bill Donohue said: "The fact that they chose Holy Week shows this is calculated, and the timing is deliberate."
Kiera McCaffrey of the Catholic League for Religious and Civil Rights further commented, "They would never dare do something similar with a chocolate statue of the Prophet Mohammed naked with his genitals exposed during Ramadan."
The decision to cut the statue from the exhibition was made by the managers of the Robert Smith hotel which housed the Manhattan gallery. They said in a statement that they wished "to affirm the dignity and responsibility of the hotel in all its affairs".
But the cancellation has prompted the resignation of the gallery's artistic director in an act of protest.
The chocolate figure stands at 6ft tall (1.8m) and shows Jesus naked hanging on the cross. Unlike usual images of Jesus hanging on the cross, the chocolate sculpture depicts Jesus without a loincloth.
