A source close to the performer told the tabloid news website TMZ: "Justin became angry at Lentz (pictured above, centre) a while ago and broke ties with the pastor.
"Justin and his fiancée, Hailey Baldwin, have both been active members of Hillsong and continue to patronise the church but, at least as far as Justin is concerned... Carl is history."
Premier has previously reported how Bieber, 24, became a Christian in Mr Lentz's New York apartment in 2014 and chose to be baptised immediately in a bath tub.
Last year, Lentz, who leads Hillsong NYC with his wife Laura, said he believed Bieber had a "deep" relationship with God.
The 39-year-old father-of-three told US Weekly Magazine: "I don't think my teaching or my preaching has made even remotely as big of an impact as his own desire and passion and love for Jesus. That's how it should work.
"The primary change agent in somebody's life, it shouldn't be a person. It shouldn't be a preacher. It should be God.
Carl Lentz with Bieber via Instagram
"I think all his changes are a credit to him and him allowing God to continue to use him. Nobody gets credit for that."
The magazine referred to the pair as BFFs, or best friends forever.
Earlier this week, Justin Bieber confirmed his engagement to Christian and model, Hailey Baldwin.
Asked by a reporter in Sydney whether he had any thoughts on the pair becoming engaged, Mr Lentz was quoted by TMZ as saying: "No".
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.