Peter Rippon handed over control while an inquiry into how the BBC dealt with the scandal is carried out, just weeks after defending his decision to axe the report in a BBC blog.
Mr Rippon originally said there was no evidence staff at the Duncroft approved school in Surrey could have known about allegations the Jim'll Fix It and Top of the Pops presenter abused children. But yesterday 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 claimed the women who spoke to his journalists had already spoken to police before the decision was taken to drop the investigation last year. The BBC now says that is untrue and Newsnight uncovered new evidence.
Mr Rippon's corrected blogpost 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: "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."
Panorama last night revealed that BBC Director General George Entwistle wrote to all staff saying the Newsnight investigation was into "Surrey Police's inquiry into Jimmy Savile towards the end of 2011".
Producer Meirion Jones replied in an email: "George –one note – the investigation was into whether Jimmy Savile was a paedophile. I know, because it was my investigation.
"We didn't know Surrey Police had investigated Jimmy Savile – no-one did – that was what we found when we investigated and interviewed his victims."
Mr Jones and reporter Liz MacKean told Panorama they had interviewed at least four of Savile's alleged victims and confirmed Surrey Police had investigated sex abuse claims against Savile in 2007.
They say when they told bosses the Crown Prosecution Service (CPS) did not charge Savile because of insufficient evidence, they were told to end the investigation and the show was withdrawn.
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."
The Newsnight journalists filmed a witness saying 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.
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."