In the interview, published in Parade magazine on Friday, John said that Jesus was "a compassionate, super-intelligent gay man who understood human problems."
"On the cross, he forgave the people who crucified him. Jesus wanted us to be loving and forgiving. I don't know what makes people so cruel," he continued. "Try being a gay woman in the Middle East -- you're as good as dead."
The comments have sparked outrage from Christian groups.
Bill Donohue, president of the Catholic League, issued a statement on the organization's Web site, saying, "Jesus was certainly compassionate, but to say He was 'super-intelligent' is to compare the Son of God to a successful game-show contestant."
"More seriously, to call Jesus a homosexual is to label Him a sexual deviant," the statement continued.
A spokesman for the Church of England told the BBC, "Sir Elton's reflection that Jesus calls us all to love and forgive is one shared by all Christians. But insights into aspects of the historic person of Jesus are perhaps best left to the academics."
The British rock star also talked about his relationship with civil partner David Furnish and his fear that "fame attracts lunatics."
"Princess Diana, Gianni Versace, John Lennon, Michael Jackson, all dead. Two of them shot outside their houses. None of this would have happened if they hadn't been famous...I never had a bodyguard, ever, until Gianni died. I don't like celebrity anymore."