A Newsnight reporter alleged that her editor tried to "kill" the Jimmy Savile story by making "impossible editorial demands" and saying the women who spoke out about the TV star were not too young at the time of the incidents.
Channel 4 News said it had seen an email sent last December by Newsnight reporter Liz MacKean in which she discusses Newsnight editor Peter Rippon's response to her investigation into Savile.
Rippon stepped aside from his job on Monday after the BBC said his explanation of why Newsnight dropped its Savile investigation was "inaccurate or incomplete".
In the email, MacKean wrote: "Having commissioned the story, Peter Rippon keeps saying he's lukewarm about it and is trying to kill it by making impossible editorial demands."
She reportedly claimed: "When we rebut his points, he resorts to saying, well, it was 40 years ago ... the girls were teenagers, not too young ... they weren't the worst kind of sexual offences etc."
MacKean, who appeared on the BBC's Panorama documentary last night, said she believed Rippon did not tell BBC1, which was planning to run Savile tributes, about the investigation.
"He hasn't warned BBC1 about the story, so they're beavering away on the special, oblivious," she wrote.
Speaking to Panorama about the decision to shelve the investigation she said: "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."
She also told Panorama: "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."
BBC director-general George Entwistle has since come under fire for not dropping the BBC's Savile tributes when he was head of BBC Vision, despite knowing that Newsnight had investigated the former TV star.
He told MPs today that he believed the Newsnight investigation should have continued.
In a statement to Channel 4 News in response to the email, the BBC said: "The BBC has confirmed it has launched an independent review lead by former head of Sky News Nick Pollard which will cover these questions.
"It would not be appropriate to comment further until these have been concluded."