Pope Francis, in a conversation with leaders of religious orders published by a Jesuit journal last Friday, said the Catholic Church had to try not to scare away children who live in complex family situations.
He was referring to those whose parents were separated and those living with gay couples.
Pope Francis gave the example of a little girl in Buenos Aires, his former diocese, who confided to her teacher the reason she was always sad was that "my mother's girlfriend doesn't like me".
The pope told the leaders of religious orders that a great challenge for the Church would be to reach out to children living in difficult or unorthodox domestic situations.
"The situation in which we live now provides us with new challenges which sometimes are difficult for us to understand," the pope said, according to the transcript of the conversation.
Italian media today ran headlines saying the Pope's words were an opening to legal provision for civil unions for gay couples, a subject of debate in Italy.
Vatican spokesman Father Federico Lombardi told Vatican Radio that media interpretations were "paradoxical" and a "manipulation" of the pope's words, particularly as some media quoted him as speaking specifically of homosexual unions, which he did not.
Father Lombardi said the pope was merely "alluding to the suffering of children" and not taking a stand on the political debate in Italy.
Since his election in March, however, the pope has avoided repeating the denunciations of homosexuality pronounced by his two immediate predecessors, Benedict XVI and John Paul II.
Last month, The Advocate, the oldest gay rights magazine in the US, named him 'Person of the Year'.
It hailed as a landmark his response last July to a reporter who asked about gay people in the Church: "If a person is gay and seeks God and has goodwill, who am I to judge?"
The Vatican has stressed the Pope's words did not change Church teachings that homosexual tendencies are not sinful but homosexual acts are.
Still, the homosexual community and many heterosexuals in the Church have welcomed what they see as a shift in emphasis and a call for the Church to be more compassionate and less damning.
Meanwhile, Pope Francis announced that he will visit Holy Land sites in Jordan, Jerusalem and the Palestinian Territories in May, his first trip to the area as pontiff.
The May 24-26 trip to Amman, Jerusalem and Bethlehem will mark the 50th anniversary of a landmark trip there by Pope Paul VI in 1964, the first by a pope in modern times. Pope John Paul II visited in 2000 and Benedict XVI went in 2009.
Pope Francis, who has made many appeals for peace in the Middle East since his election in March, announced the trip to thousands of people in St. Peter's Square for his Sunday address.
He was invited by both Palestinian President Mahmoud Abbas and Israeli President Shimon Peres.