Juan Carlos Cruz, the main whistleblower in Chile's clerical sex abuse and cover-up scandal, said on Monday he spoke to Francis about his homosexuality during their recent meetings at the Vatican.
The pope invited Mr Cruz and other victims of a Chilean predator priest to discuss their cases last month.
Mr Cruz said he told Francis how Chile's bishops used his sexual orientation as a weapon to try to discredit him, and of the pain the personal attacks had caused him.
"He said, 'Look Juan Carlos, the pope loves you this way. God made you like this and he loves you'," Mr Cruz said.
The Vatican declined to confirm or deny the remarks in keeping with its policy not to comment on the pope's private conversations.
The comments first were reported by Spain's El Pais newspaper.
Church teaching says gays should be respected, loved and not discriminated against, but considers homosexual activity "intrinsically disordered".
Francis, though, has sought to make the church more welcoming to gays, most famously with his 2013 comment "Who am I to judge?"
He also has spoken of his own ministry to gay and transgender people, insisting they are children of God, loved by God and deserving of accompaniment by the church.
As a result, some commentators downplayed the significance of the comments to Mr Cruz, saying they merely were in line with Francis' pastoral-minded attitude and not in any way a challenge to current doctrine.
"What the pope was saying is, 'God loves you and made you just as you are, and therefore you should accept yourself as you are while struggling to live according to the Gospel,'" said Father Robert Gahl, a moral theologian at Rome's Pontifical Holy Cross University.
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