Speaking to the Spanish newspaper El Pais, Juan Carlos Cruz said that the admission came during a conversation in the Pope's private apartments where he was staying with two other Chilean abuse victims during a visit to the Vatican earlier this month.
"God made you like that and he loves you like that and I do not care".
If reported accurately, the pope's comments mark a distinct break from over 2,000 years of Catholic teaching, which considers homosexuality "objectively disordered" and in contradiction to God's law.
Juan Carlos Cruz spoke with the pope a few weeks ago about abuse he suffered from the Chilean priest, Fernando Karadima.
Cruz confirmed that they did speak about homosexuality, and that he explained to the Pope that he is not a bad person and tries not to hurt anybody.
Cruz, a victim of a predator priest, said he had been discredited by Chile's bishops for being gay and told Francis of the pain their slander caused.
"He told me, 'Help me so that the Holy Spirit guides me so that I know well what I have to do, '" Cruz said.
"The important thing is that the Church be a woman, that [it] has this attitude of a bride and of a mother", he said, adding that "when we forget this, it is a masculine Church".
Some of the Vatican investigator's findings were included in the report, according to Chile's T13 television, which acquired a leaked copy.
In a speech to an annual assembly of the Italian bishops conference Monday, Francis blamed the priest shortage on such factors as demographic changes, scandals in the church and cultural trends that dissuade young people from making lifelong commitments and make them value instead the "dictatorship of money".
"The Spirit frees hearts chained by fear", the Pope said in his homily. "When they say 'Oh, how great, how great, how great, ' that's not useful". Not to say that it's all the same, but in each case, welcome, accompany, study, discern and integrate.
Francis said the primary distinctive quality of a woman is tenderness, which can be seen in Mary's act of wrapping her newborn son "in swaddling clothing" and laying him in the manger in Bethlehem.
A year later, Pope Francis released the 256-page document "The Joy of Love", which encouraged individual conscience to be the guiding principle for Catholics negotiating the complexities of sex, marriage and family life.