In an interview with HBO news platform Axios, the 44-year-old said: "If you're not living according to the teaching of the Bible, and you're living in unrepentant sin, then you have to be put out of the church. I excommunicated myself, essentially."
He refused to say what his "unrepentant sin" is.
The author of the popular 1997 book, I Kissed Dating Goodbye, said he came to realise that he gave bad advice in his many books.
He said: "In an effort to set a high standard, the book emphasised practices (not dating, not kissing before marriage) and concepts ... that are not in the Bible.
"I apologised for it. I unpublished the books. I pulled the books off the market. But you can't give people [back], you know, years of their life. It was a long process for me. I started seeing that the book really had misled a lot of people."
Harris, who left his role as lead pastor of a church in 2015, now spends his Sunday mornings doing yoga.
"I was a leader and a spokesman and I called people to live in very particular ways, to sacrifice in very particular ways," he said.
"And so for me to change in my thinking feels like a betrayal to them.
"I was really just trying to be honest about the fact that all the ways that I had defined faith and Christianity, that I was no longer choosing to live according to those."
Harris added: "Someone said, 'I don't believe in God, but I miss Him.' I can relate to that."
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