At a time when most of the BBC's journalists, including many of its best-known presenters, are out on strike, Thompson has been dealt a damaging blow by one of the most powerful figures in the BBC newsroom, who has accused the Director-General of undermining the organisation's reputation for impartiality.
Stephen Mitchell, deputy director of news at the BBC, told an audience at the University of Kent that Thompson's decision to sign a letter to Vince Cable, calling on the Business Secretary to intervene in the proposed takeover of BSkyB by Rupert Murdoch's News Corporation, compromised the ability of BBC journalists to cover an important story.
Thompson was a joint-signatory to the letter along with representatives of several commercial media organisations, including the publishers of the Daily Mail, the Daily Telegraph, The Guardian and the Daily Mirror. The BBC's governing body, the BBC Trust, has already expressed concern that it was not consulted by Thompson before he signed the document.
Mitchell, who is also the BBC's head of multimedia programmes, said: "The BBC has to above all be impartial and almost as importantly be seen to be impartial in every issue of controversy in the UK. It is inevitable that we will cover the growth and role of News Corp going forward as part of our journalism.
"Mark Thompson is the editor-in-chief and I feel that that letter in a way compromises the perception of his impartiality on an issue of current controversy... For me, he compromises his role in life by signing a letter in the way that he did."
Mitchell, who was speaking at the Centre for Journalism at the University of Kent, and responding to a question from third-year journalism undergraduate John Saunders, was aware that his comments were on the record.
In a brief statement last night, the BBC said that Mitchell "attended this event in a personal capacity and the views expressed were his own".
In addition to Mitchell's criticism, his boss, Helen Boaden, the BBC director of news, has attacked the way that Thompson and his senior management team have handled BBC employees' pensions. In a leaked email, Boaden says: "All I can say is that as a pension Trustee, I think it would have been much, much better if the BBC had waited for the deficit to be properly assessed and then worked with the Trustees to come up with a viable long term plan for addressing it." The National Union of Journalists, which is staging the strike over planned changes to the BBC pension scheme, released the email and said that it agreed with Boaden.
The strike, during which BBC bulletins have been presented by freelance presenters little known to much of the audience, has come at the end of a week in which the corporation's journalism has suffered a major blow in the form of a humiliating apology issued over a World Service story that wrongly claimed that millions of pounds raised by Bob Geldof's charity Band Aid to help starving people in Ethiopia had been diverted to buy arms. The former BBC chairman Michael Grade, a trustee of the Band Aid Trust, described the broadcast as "a terrible, terrible mistake, they've damaged 24 years of work [and] they've damaged the public perception of giving aid to relieve starving people around the world".
The corporation is still reeling from last month's dramatic negotiations with the Government that saw Thompson and the BBC Trust chairman Sir Michael Lyons forced to accept a 16% cut in budget and a freeze on the licence fee for the next six years.
Many believe that Thompson and his negotiating team were bounced into accepting the cuts after the government confronted them with the possibility of paying the £556m a year cost of providing free licences to the over-75s, a prospect which the Newsnight political editor Michael Crick described as a "bombshell" and which senior BBC insiders have said sent the organisation into "meltdown".
Yesterday, as part of a skeleton service on Radio 5 Live, the BBC repeated an interview with the Culture Secretary Jeremy Hunt, who brokered that deal with Thompson.
As it was, programmes including the flagship Radio 4 Today programme were taken off air yesterday. Boaden herself was obliged to file a news report for Radio 4's lunchtime news.
Thompson was mocked by the NUJ for his handling of the dispute and his defence of yesterday's BBC's output. The union's general secretary Jeremy Dear compared him to Comical Ali, the former Iraqi Information Minister Mohammed Saeed al-Sahhaf, who denied the presence of American troops in Baghdad during the invasion of Iraq.
Media observers are increasingly unimpressed with Thompson's record. "The BBC is confronted with the success of Sky and Murdoch and his billion-pound profits and needs to be in a fit state to carry out its public service role, but instead we see a series of fiascos and disasters," said Paul Lashmar, acting head of journalism at Brunel University.
"Everything that Mark Thompson seems to do only undermines the morale in his newsrooms and leaves the BBC's journalists feeling that they are lions led by donkeys."
Among striking journalists yesterday, there was some sympathy for Thompson, who is a BBC employee of 31 years' experience and a journalist of distinction, having edited the Nine O'clock News and Panorama. Strikers criticised the handling of the dispute by the BBC's human resources chief Lucy Adams and the group finance director Zarin Patel.
The director-general, who recently took a £163,000 cut from his £838,000 annual remuneration, was appointed in 2004 and is understood to want to serve 10 years in the role.
Responding to criticism of BBC executive salaries, he has recently made cuts to the corporation's senior management, including parting with his deputy Mark Byford. But those that have left the upper echelons of the BBC have not been the director-general's strongest critics and he is likely to face internal challenges to his position.
Which famous names did (and didn't) strike
The Newsnight economics editor Paul Mason joined the picket lines and accused BBC management of "trying to steal" journalists' pension benefits. While protesting he came face-to-face with the BBC's (outgoing) deputy director-general Mark Byford, who ignored requests from strikers to speak as he walked through them. Other presenters including Five Live's Nicky Campbell and newsreaders Fiona Bruce and Huw Edwards joined the action.
Among those who broke the strike were Business Editor Robert Peston and Royal & Diplomatic correspondent Nicholas Witchell. Andrew Neil presented BBC Two's Daily Politics, beginning: "Don't bother sending me emails today...I'm just not in the mood to read them out."
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