The Times has reported on a leaked internal email, sent by a junior press officer at the BBC, which appeared to contradict the BBC's official statement on why the investigation was shelved last December.
Allegations of sexual abuse against the late Savile were aired in an ITV documentary last month, leading to a police investigation and claims that there could be more than 30 victims of the former Jim'll Fix It host.
The leaked BBC email reveals that the Newsnight investigation was at a very advanced stage when it was dropped as the press officer Helen Deller was preparing "lines to take" in response to potentially hostile media inquiries.
It also reportedly indicates that journalists at Newsnight were "focusing on allegations of abuse" against Savile. The email was sent on December 7 to Peter Rippon, the Newsnight editor, and Meirion Jones, an "investigations producer" on the programme.
Rippon has always maintained that the investigation was focused on establishing whether there was an "institutional failure" by the police or Crown Prosecution Service to fully investigate the claims against Savile.
He previously said that the story was dropped because there was insufficient evidence to support such a failure, which meant that the report had been "weakened from a Newsnight perspective".
A BBC spokesman said in response that the "ridiculous story in no way casts doubt on what the BBC has previously said on this".
He added: "It is simply an exchange between a junior press officer and the Newsnight producer asking for further information about the Jimmy Savile investigation.
"This email exchange along with other relevant documents will be passed to the Pollard inquiry."
The BBC has announced two major investigations into its handling of the allegations against Savile.
Former High Court judge Dame Janet Smith will lead one inquiry, focused on the culture and practices of the BBC while Savile worked at the corporation.
Nick Pollard, the former Head of Sky News, will head the second inquiry, regarded as urgent, which will "seek to establish whether there were any failings in the BBC's management of the Newsnight investigation relating to allegations of sexual abuse of children by Jimmy Savile, including the broadcast of tribute programmes on the BBC".
> Newsnight "inappropriately pulled" Savile report, says culture secretary Maria Miller
On Monday night (October 22), the BBC Panorama programme will also air an investigation into Newsnight's decision to drop the report on Savile.
Meanwhile, a previously unpublished interview has emerged with Savile in which the TV star is quoted as admitting he was "not a straight punter".
The Jewish Chronicle obtained a transcript of the interview, which included Savile allegedly telling a freelance reporter: "When I'm gone, they'll say, 'I always thought he was straight but he wasn't - he was crooked'."