But 28 years after his death, in an interview being broadcast for the first time, he claims that on the contrary, he hoped to encourage people to focus on the Christian faith.
Despite his familiar image as a hippy icon who invited us to imagine a world without religion, Lennon says he was "one of Christ's biggest fans" and felt emotional in church.
In the interview, which was recorded in 1969 and is being aired on BBC Radio 4's Sunday programme, he talks about the Church of England, his vision of heaven, and expresses disappointment at not being allowed to marry his second wife, Yoko Ono, in church.
The interview was conducted by Ken Seymour of the Canadian Broadcasting Corporation when Lennon and Ono were at the Bed-In for Peace protest in Montreal. It was bought three years ago by National Museums Liverpool, which is playing an extract at a new exhibition at World Museum Liverpool.
Christians around the world had been dismayed by Lennon's boast in an article in London's Evening Standard about the popularity of the Beatles, but the singer says he was misunderstood.
"It's just an expression meaning the Beatles seem to me to have more influence over youth than Christ," he says. "Now I wasn't saying that was a good idea, 'cos I'm one of Christ's biggest fans. And if I can turn the focus on the Beatles on to Christ's message, then that's what we're here to do."
He blames "the hypocrites" for being too "uptight" in reacting to his comments. "If the Beatles get on the side of Christ, which they always were, and let people know that, then maybe the churches won't be full, but there'll be a lot of Christians dancing in the dance halls. Whatever they celebrate, God and Christ, I don't think it matters as long as they're aware of Him and His message."
He acknowledges a strong belief in the power of prayer but says he dislikes all the church trappings. "Community praying is probably very powerful… I'm just against the hypocrisy and the hat-wearing and the socialising and the tea parties."
His aversion to institutional religion was shaped when a "ludicrous" vicar banned him from a church when he was 14 because he and his friends were "having the giggles".
"I wasn't convinced of the vicar's sincerity anyway. But I knew it was the house of God. So I went along for that and the atmosphere always made me feel emotional and religious or whatever you call it.
"Being thrown out of church for laughing was the end of the Church for me."
He continues: "I would have liked to have been married in a church but they wouldn't marry divorcees… That's pure hypocrisy." The Church's position on the issue changed in 2002.
On heaven, he says: "I haven't got any sort of dream of a physical heaven where there's lots of chocolate and pretty women in nightgowns, playing harps. I believe you can make heaven within your own mind. The kingdom of heaven is within you, Christ said, and I believe that."
The author Paul Du Noyer, who has written extensively on the Beatles, said: "He was chastened by the reaction he got to his Jesus remarks and it probably made him think more carefully about religion.
"These comments would have been a great boost for churches if they had come out at the time."