Pope Francis declared on Monday that it was not his place to judge homosexuals and said they should not be marginalised but condemned the gay lobby as a "serious problem".
The remarks -- made to journalists as he flew back to Rome from a trip to Brazil -- appeared to be more conciliatory towards homosexuals than his predecessor Benedict XVI.
"If someone is gay and seeks the Lord with good will, who am I to judge?" he said
"The problem is not having this orientation, it is lobbying. That's the most serious problem I think."
Francis had to field questions about Battista Ricca, who was appointed by the pontiff to a key position at the troubled Vatican bank, but is embroiled in allegations that he had gay relationships with male prostitutes.
The pope said he had ordered a "brief investigation but we found nothing on him".
"I have not seen anyone at the Vatican who is registered as gay on his identity card. We acknowledge that there are (gays)," he said.
Nevertheless, "the catechism of the Catholic Church says clearly that we must not marginalise these people who should be integrated in the society."
The Italian weekly L'Espresso this month reported that Ricca had gay relationships during his time at the Vatican embassy of Montevideo in Uruguay as well as an affair with a Swiss guard which ultimately saw him sent back to Rome in disgrace in 2010.
He was once left badly beaten after trawling notorious gay hangouts and also had to be rescued from an elevator in which he was stuck while he was with a young gigolo he had invited to the embassy for the night.
An internal bid to cover up Ricca's activities meant Francis apparently had no idea about Ricca's past before he appointed him as his personal representative at the scandal-hit bank this year.
The pope admitted in June that there is a "gay lobby" in the Vatican's secretive administration, the Roman Curia, according to a Latin American Catholic website.
Gay rights groups had voiced hope on Francis' appointment that the Argentinian pope would be friendlier to homosexuals than his predecessor.
Benedict had angered the gay community with his suggestion in 2008 that homosexuality was as much of a threat to the survival of the human race as climate change.
He has also called on Catholics to "fight" to maintain the traditional family consisting of a father, mother and children, and criticised gay marriage and abortion as "insidious and dangerous threats to the common good".
Without expanding on the two issues, Pope Francis gave a firm answer to a question on gay marriage and abortion -- both of which the Church opposes -- saying "you know perfectly the position of the Church".
He also said women should be given a bigger role in the Church, but refused to consider their ordination, saying the "door is closed" on the issue.