He has handed over control of the flagship current affairs show while an inquiry into how the BBC handled the scandal is carried out.
Earlier this month, Mr Rippon defended his decision to axe the report in a BBC blog but the corporation has now issued a correction.
He originally said there was no evidence staff at the Duncroft approved school could have known about allegations Savile abused children, but the BBC said: "In fact some allegations were made (mostly in general terms) that some of the Duncroft staff knew or may have known about the abuse."
Mr Rippon also said the women who spoke to Newsnight journalists had already spoken to police, but the BBC now says that is untrue and Newsnight actually uncovered new evidence about Savile's alleged crimes.
The corrected blogpost also said that while no allegations were made BBC staff "were aware" of Savile's behaviour, Newsnight did hear allegations of "abusive conduct on BBC premises".
A BBC spokesman said: "On the basis of material now available, it is apparent from information supplied by the Newsnight editor and programme team that the explanation by the editor in his blog of his decision to drop the programme's investigation is inaccurate or incomplete in some respects."
The Prime Minister said the announcement Mr Rippon had stood aside and that his account of why the programme was dropped was rewritten raised "serious questions".
It comes after excerpts from tonight's edition of Panorama highlighted the different explanations given by BBC bosses about the nature of the documentary and why it was dropped.
In the aftermath, BBC director-general George Entwistle wrote to all staff saying that the Newsnight investigation was into "Surrey Police's inquiry into Jimmy Savile towards the end of 2011".
But producer Meirion Jones immediately emailed Mr Entwistle countering that, writing: "George - one note - the investigation was into whether Jimmy Savile was a paedophile - I know because it was my investigation.
"We didn't know that Surrey Police had investigated Jimmy Savile - no-one did - that was what we found when we investigated and interviewed his victims."
Mr Entwistle will appear before a parliamentary select committee tomorrow to answer questions about the corporation's handling of the scandal.
Tonight's hour-long documentary, which goes out on BBC1 at 10.35pm, will hear from Mr Jones and reporter Liz MacKean, who both claim they interviewed at least four alleged victims of Savile - and confirmed with Surrey Police they had investigated sex abuse complaints against the Jim'll Fix It star in 2007.
They say when they told bosses the Crown Prosecution Service did not charge Savile because of insufficient evidence, they were told to end the investigation - and the show was withdrawn.
The horror stories about Savile emerged only after ITV broadcast a documentary at the start of this month - sparking mayhem at the BBC over losing its scoop and leading to the allegations of a cover-up.
A Panorama statement said: "Peter Rippon has always maintained the story was pulled for 'editorial reasons' and not because of a potentially embarrassing clash with planned BBC tributes to Savile over Christmas.
"Panorama has found no evidence to contradict that view."
Mr Jones and Ms MacKean tell programme-makers bosses wanted them to stand up a suggestion Savile was not prosecuted because the Crown Prosecution Service thought he was too old and frail.
When it emerged that was not true and he was not prosecuted because of insufficient evidence, the pair were told to abandon the investigation rather than get more proof, Panorama reports.
Ms MacKean said: "Ever since the decision was taken to shelve our story, I've not been happy with public statements made by the BBC.
"I think they're very misleading about the nature of the investigation we were doing."
The Newsnight journalists filmed Karin Ward, a key witness, in mid-November saying that Savile abused her during her time at Duncroft.
She claims she saw pop star Gary Glitter having sex with another under-age girl from Duncroft on BBC premises.
Newsnight quoted three other unnamed former Duncroft pupils who said they were also sexually abused by Savile. The script included a report of sexual abuse of a teenager at Stoke Mandeville Hospital.
Ms MacKean said Mr Rippon suddenly went cold on the story: "All I can say is that it was an abrupt change in tone from, you know, one day 'Excellent, let's prepare to get this thing on air' to 'Hold on'."
She says she was left with the clear impression her editor was feeling under pressure, writing to a friend: "PR (Peter Rippon) says if the bosses aren't happy... (he) can't go to the wall on this one."
Ms MacKean told Panorama: "I was very unhappy the story didn't run because I felt we'd spoken to people who collectively deserved to be heard and they weren't heard and I thought that was a failing... I felt very much that I'd let them down."
The programme also reveals BBC director of news Helen Boaden told Mr Entwistle - at that time director of vision - about the Newsnight investigation and its possible impact on planned tributes to Savile during an awards lunch on December 2.
She told him that if the Newsnight investigation went ahead, he might have to change the Christmas schedules.
Mr Jones emailed Mr Rippon five days later to warn him about what would happen if the investigation was dropped.
"I was sure the story would come out one way or another and that, if it did, the BBC would be accused of a cover-up," Mr Jones tells Panorama.
"In fact, I wrote an email to Peter saying 'the story is strong enough' and the danger of not running it is 'substantial damage to BBC reputation'."
Two days later, Mr Rippon decided to kill the investigation, Panorama reports.
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