The Pope has been sensationally quoted as saying hell does not exist and souls not worthy of heaven merely disappear instead of being tormented.
But the Vatican quickly denied the apparent dramatic theological shift, accusing atheist reporter Eugenio Scalfari of "reconstructing" his words.
Catholic teaching dictates that "immediately after death the souls of those who die in a state of mortal sin descend into hell".
Scalfari, 93, in his fifth interview of Pope Francis published in the La Repubblica newspaper, asked what happened to "bad souls" after their bodies died.
"They are not punished, those who repent obtain the forgiveness of God and enter the rank of souls who contemplate him, but those who do not repent and cannot therefore be forgiven disappear," he quoted the Pope as replying.
"There is no hell, there is the disappearance of sinful souls."
The Vatican on Thursday said the Italian journalist and the Pope had a private meeting but claimed it was "without giving him any interview".
"What is reported by the author in today's article is the result of his reconstruction, in which the literal words pronounced by the Pope are not quoted," it said.
"No quotation of the aforementioned article must therefore be considered as a faithful transcription of the words of the Holy Father."
The Holy See pointed out that Pope Francis previously mentioned hell in a March 2014 prayer vigil calling on mafia members to change their lives.
"While there is still time, so that you do not end up in hell. That is what awaits you if you continue on this path," he said then.
Scalfari has previously been accused of contorting the Pope's words in previous meetings, because of his unconventional style of not taking notes.
"I try to understand the person I am interviewing, and after that I write his answers with my own words," he said after a 2013 incident.
He at that point reported the Pope told him: "Everyone has his own idea of good and evil and must choose to follow the good and fight evil as he conceives them."
Scalfari afterwards conceded that as a result "some of the Pope's words I reported, were not shared by Pope Francis".
The following year Vatican officials even questioned whether reports of interviews with the Pope by atheist reporters could ever be trusted.