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.
"How can we proclaim Christ to these boys and girls? How can we proclaim Christ to a generation that is changing? We must be careful not to administer a vaccine against faith to them," he said.
Italian media on Sunday 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.
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 United States, 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 gay 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.
(Reporting By Philip Pullella; Editing by Sophie Hares)