The singer also told Parade Jesus was "compassionate", forgiving and "understood human problems".
A spokesman for the Church of England said: "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," he added.
Sir Elton said in the interview: "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. Try being a gay woman in the Middle East - you're as good as dead," he added.
In the interview, the singer also said he did not like being a celebrity any more because "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," he said.