The Pope reportedly used a derogatory term about gay men in a private meeting with bishops, where he is said to have reiterated they should not be allowed to become priests.
The Vatican has apologised after the Pope used a highly offensive word about gay men.
In a statement, it said: "Pope Francis is aware of the articles recently published about a conversation, behind closed doors, with the bishops of the CEI [the Italian Episcopal Conference of Catholic bishops].
"As he stated on several occasions, 'In the Church there is room for everyone, for everyone! Nobody is useless, nobody is superfluous, there is room for everyone. Just as we are, all of us.'
"The Pope never intended to offend or express himself in homophobic terms, and he apologises to those who felt offended by the use of a term reported by others."
Pope Francis made the remark in a closed-door meeting with bishops, when describing priesthood colleges as already too full of "frociaggine" – a highly offensive Italian slur.
He is said to have reiterated that gay men should not be allowed to become priests.
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The remark was reportedly made on 20 May, as first reported by political gossip website Dagospia, when the Italian Bishops Conference held a private meeting with the Pope.
"It's all the fault of some bishop who broke his mandate of silence to report the gaffe that occurred last week," reported Il Messaggero, a national paper based in Rome.
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According to the paper, the Pope's comments came during an informal Q&A session at the annual bishops' meeting which was attended by more than 200 members of the clergy.
Some seeking to defend His Holiness have said that Spanish and not Italian is his first language, and the Pope has made linguistic gaffes in the past when speaking in a language other than his mother tongue.
The 87-year-old Argentinian often speaks informally, jokes using slang and even swears in private, according to reports.
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The Pope has been credited with leading the Roman Catholic Church into taking a more welcoming approach towards the LGBT+ community.
At the start of his papacy in 2013, he said: "If a person is gay and seeks God and has good will, who am I to judge?"
Last year, he allowed priests to bless same-sex couples, triggering significant conservative backlash.
But in 2018, he told Italian bishops to carefully vet priesthood applicants and reject anyone suspected of being gay.
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In a 2005 document, during Benedict XVI's papacy, the Vatican said the church could admit into the priesthood those who had overcome gay tendencies for at least three years.
But the document also said those with "deep-seated" gay tendencies and those who "support the so-called gay culture" should be barred.
By Adam Parsons, Europe correspondent
This is not the first time the Vatican has issued an apology.
But they don't normally come quite so quickly. Unprecedented, according to one Vatican observer.
Still, this had the marks of having gone through the lawyers first.
Firstly, the statement comes from the Holy See, rather than Pope Francis himself.
Then there's that way of phrasing it that we've all heard previously from politicians – he apologises to those who felt offended, rather than simply saying he got it wrong. It doesn't feel very contrite.
There is no denial, even if the offensive expression is described, dispassionately, as "a term used by others". But for all the caveats, there is something remarkable here – an admission that this was a misstep that needed correcting.
And the Vatican knows that this will be seen as a tacit admission that the Pope did use this expression – a truly offensive slur that would sound bad enough if it was said by a dunderhead in a bar, but which actually came out of the mouth of the leader of the Catholic Church.
Pope Francis was already facing questions over his health and his ability to hold the church together. Those questions may now be asked a little louder.
