"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.