The Newsnight producer behind the dropped Sir Jimmy Savile investigation warned his editor that the BBC was at risk of being accused of a cover-up.
Meirion Jones told the Panorama programme looking into the Savile scandal that he had emailed Newsnight editor Peter Rippon on 7 December 2011.
"I was sure the story would come out one way or another and... the BBC would be accused of a cover-up," he said.
The BBC says it will not comment while an investigation takes place.
Police have launched a criminal inquiry after saying that former BBC presenter and DJ Savile, who died in October 2011 aged 84, may have sexually abused many people, including young girls, over a 40-year period - sometimes on BBC premises.
They are investigating about 400 lines of inquiry which may involve other offenders.
Allegations regarding Savile's conduct came to light following an ITV investigation broadcast on 3 October - nearly 10 months after it had emerged that a similar Newsnight report had been axed by the BBC.
In a chain of emails between Newsnight journalists and Mr Rippon, Mr Jones said his editor's emphasis on what the programme's report was about changed from revealing Savile as a paedophile to being about establishing why the Crown Prosecution Service (CPS) had dropped an investigation into sexual abuse claims regarding Savile made by several women.
Mr Rippon later said he felt the story had fallen short and decided not to pursue it further.
He stressed in a posting on the BBC Editors' blog that he was in no way pressured into his decision because of a potentially embarrassing clash with the planned BBC tributes to Savile over Christmas 2011.
Panorama found no evidence to contradict that view.
Mr Rippon stressed in his blog that the story had been pulled for editorial reasons, arguing the story would have been much stronger if Newsnight could have proven some institutional failure by the police - which it had failed to do.
The Newsnight editor has not responded to the points Panorama has raised.
BBC director general George Entwistle has announced two inquiries regarding the sex abuse claims.
The first is looking at why the Newsnight investigation was shelved and is being led by Nick Pollard. It is expected to report in December.
The second will be led by former Court of Appeal judge Dame Janet Smith DB and will examine the culture of the BBC during the years that Savile worked there. The results are expected in spring 2013.
Panorama found that at an awards luncheon at the Hilton hotel on 2 December 2011, BBC director of news Helen Boaden told Mr Entwistle, the then director of Vision - which oversees BBC TV commissioning and programming - about the Newsnight investigation and its possible impact on the planned tributes to Savile.
Ms Boaden told him that if the Newsnight investigation went ahead, he might have to change the Christmas schedules. The conversation is said to have taken "less than 10 seconds".
'Questions to answer'
Both Mr Entwistle and Ms Boaden have not provided responses to the points raised by Panorama.
John Whittingdale, chairman of the Commons Culture, Media and Sport Committee - which will take evidence from the director general on Tuesday - said the reasons for dropping the Newsnight report remained unclear and insisted Mr Entwistle had serious questions to answer.
Speaking to BBC Radio 4's Today programme, Mr Whittingdale said: "If you were the director of Vision, you were told at the time you were commissioning programmes paying tribute to Jimmy Savile that Newsnight might be about to reveal a bombshell, you wouldn't just have a 10-second conversation.
"You'd say, 'tell me more, I'm about to go public putting out these programmes making out that Jimmy Savile was this saint'.
"And yet it appears from this he didn't even ask a question about what the Newsnight investigation was about."
Both Mr Jones and fellow Newsnight journalist Liz MacKean told Panorama that the story they had worked on for a month was halted when they felt it was close to transmission.
Mr Jones said he was certain the story would eventually come out and the BBC would be accused of a cover-up.
"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'."
Liz MacKean said of Mr Rippon's decision to drop 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 added: "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."
Ms MacKean also expressed concern about how the decision to abandon the story has been portrayed at the highest levels of the BBC as being about Surrey Police's investigation.
Speaking to Panorama she said: "Ever since the decision was taken to shelve our story, I've not been happy with the public statements made by the BBC. I think they're very misleading about the nature of the investigation we were doing.
"The story we were investigating was very clear cut. It was about Jimmy Savile being a paedophile and using his status as a charity fundraiser and television presenter to get access to places where there were vulnerable teenage girls he could abuse."
Speaking to the BBC, Radio 4's Media Show presenter, Steve Hewlett, said the way the organisation had explained its reasons for dropping the Newsnight report were at best partial and arguably misleading - and had fuelled suspicion about corporate influence in the decision.
'Trust of people'
On 5 October 2012, the BBC's Mr Entwistle wrote to staff about the controversy: "The BBC Newsnight programme investigated Surrey Police's enquiry into Jimmy Savile towards the end of 2011."
Mr Jones immediately emailed Mr Entwistle taking issue with that account. He wrote: "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."
Veteran BBC foreign editor John Simpson said the questions swirling around the BBC's handling of the Newsnight investigation is the worst crisis to hit the public broadcaster in his almost 50-year career.
"All we have as an organisation is the trust of the people, the people that watch us and listen to us and if we don't have that, if we start to lose that, that's very dangerous I think for the BBC."
Panorama: Jimmy Savile - What the BBC Knew, BBC One, Monday, 22 October at 22:35 BST and then available in the UK on theBBC iPlayer.