The failure of BBC2’s Newsnight to run its investigation into Jimmy Savile has exposed the divisions and faultlines within the programme and affected morale within BBC News, sources have alleged.

One senior figure described a “febrile atmosphere” within news and current affairs, while others said that factions within BBC News are seriously disrupting morale and performance.

Newsnight editor Peter Rippon is understood to have lost confidence in a section of his team and the decision by Newsnight reporters to turn on him and take part in the Panorama programme is indicative of wider tensions in the department.

One Newsnight source said people working on the programme feel “let down by management”, and described how the Savile debacle has renewed fears that the programme is “under threat”.

Questions about the future of Newsnight have been raised previously and it has attracted more that 1 million viewers on just four occasions this year, compared with 14 times in 2011.

Panorama’s decision to pick up the investigation in Jimmy Savile: What The BBC Knew, which achieved 5 million viewers (39% share), was interpreted by some as a journalists’ rebellion against corporate management. Panorama editor Tom Giles ordered the film, which one BBC News source said was “an autonomous decision and a real kick at Newsnight”.

Sources close to both Panorama and Newsnight believe that Giles and BBC World Service director Peter Horrocks will emerge as winners as the fallout from the scandal continues, with suggestions they have felt “sidelined” by director of BBC news Helen Boaden in recent years. However, a senior Panorama source rejected that analysis as “silly”, pointing out that Boaden appointed Giles to the Panorama job more than two years ago.

The source acknowledged that Boaden was “far more focused on daily news than on Panorama” but added that her position was “perfectly respected by the programme, and relations are generally fine”.

In his evidence to the Culture, Media and Sport select committee, Entwistle fended off a question from MP Paul Farelly suggesting that the BBC was “at war” with itself. However, he admitted: “There is no question there was a significant breakdown in communication at Newsnight on the subject of this investigation.”

Insiders have also noted that Newsnight is not thought to have shared its failed investigation with other BBC journalists, which  might have allowed them to pick up the story sooner or prompted more questions about why their investigation was shelved.