It comes as the Prime Minister and Culture Secretary added their voices to growing criticism over the £450,000 pay-off given to former director-general George Entwistle, calling it “hard to justify” in the wake of the botched investigation by the BBC’s current affairs show.
Mr Entwistle, who resigned on Saturday, has been awarded a full year’s pay after bowing out 54 days into his reign, despite normally being entitled to only half that figure.
BBC Trust chairman Lord Patten yesterday defended the sum, saying it was “justified and necessary” to allow a clean break and avoid lengthy delays.
The settlement was discussed in Parliament on a further day of drama which saw two senior figures - BBC director of news Helen Boaden and her deputy Stephen Mitchell - step aside from their posts temporarily.
Last night, the official report into the botched Newsnight programme by the BBC’s Scotland director Ken MacQuarrie found there was confusion about who had the ultimate responsibility for “final editorial sign-off” on the story which falsely linked Lord McAlpine to a paedophile ring.
In the report, he said the programme’s editorial management structure had been “seriously weakened” as a result of the editor having to step aside over the Jimmy Savile scandal, and the departure of the deputy editor. Mr MacQuarrie added that there were shortcomings in the quality of the journalism.
He said: “During the editorial decision-making process, some of the basic journalistic checks were not completed.
“Specifically, identification was not confirmed by photograph with the first victim. The second victim could not be traced in order to provide up-to-date corroboration.”
Although legal advice was sought over the report, no right of reply was offered to the unnamed individual at the centre of the allegation.
The programme featured an interview with Steve Messham, an abuse victim who said a senior political figure of the time abused him. He later said he wrongly identified his abuser and apologised.
The BBC said Peter Johnston, director of BBC Northern Ireland, had been involved in the decisions about the Newsnight report.
London mayor Boris Johnson said there should be a “wholesale massacre of everybody involved professionally speaking” but backed Lord Patten to keep his role.
He told ITV1’s The Agenda with Tom Bradby there had been “an absolutely catastrophic breakdown of journalistic standards” surrounding Newsnight that meant other heads should roll.
“First of all, they ignored the Savile scoop which they were sitting on, and it seems like they had quite a lot of evidence and then they had this crazy switching the steering wheel in the other direction and going for some ‘top Tory paedo’ without any real evidence.
“It was absolutely disastrous.”
The BBC Trust said Mr MacQuarrie’s findings of “serious failures” were “very concerning”.
A spokeswoman said: “It is clear from the MacQuarrie report on the November 2 Newsnight that there were serious failures in the normal checks and balances that the trust expects from BBC journalism, and these were compounded by the confusion created by the dual reporting structure in news established during the Pollard inquiry. This is very concerning.”
Acting director-general Tim Davie has set about to trying to restore confidence in the broadcaster, claiming his role was “to get a grip of the situation”.
Mr Davie addressed staff by email yesterday telling them he was “determined to give the BBC the clarity and leadership it deserves”, and said management would pull together as “one team”.
He also pledged to personally apologise to Lord McAlpine following the resignation of Mr Entwistle, who has been given 12 months’ pay - the amount he could have expected if he was sacked - rather than the six-month figure he was entitled to under his contract. The extra money is equivalent to the income from 1,546 licence fees.
In the House of Commons yesterday, Culture Secretary Maria Miller described it as a “reward for failure” but said ultimately it was a matter for the BBC Trust to decide the figure.
The payment was described as “outrageous” by some MPs, and a spokesman for David Cameron said it was “hard to justify”.
But in a letter to John Whittingdale, chairman of the Commons Culture, Media and Sport Committee, Lord Patten said the payment was agreed to avoid “long drawn-out discussions and continuing uncertainty”.
The BBC said the announcement that Ms Boaden and Mr Mitchell had stepped aside was not as a result of the Newsnight programme this month.
Instead, they were in response to the “lack of clarity” surrounding who is in charge while the Pollard Review is making its inquiries.
This review - led by former Sky News chief Nick Pollard - is looking into an earlier decision to shelve a Newsnight investigation into Savile’s sexual abuse.
The BBC’s head of news gathering, Fran Unsworth, and Ceri Thomas, the editor of the Radio 4 Today programme, are to fill in for Ms Boaden and Mr Mitchell temporarily.
Karen O’Connor, a former deputy editor of Panorama and Newsnight, has been drafted in as acting editor of Newsnight.
Yesterday also saw the resignation of Iain Overton as editor of the Bureau of Investigative Journalism over its involvement with the November 2 Newsnight programme.
Mr Overton tweeted before the start of the programme that Newsnight would feature an item, which the BIJ worked on, about a “senior political figure” who was said to be a paedophile.
It led to rumours circulating about the identity of the figure in question, eventually linking it to Lord McAlpine’s name, although the story proved to be untrue.
In a letter to The Times, the trustees of the BIJ said it an inquiry has been launched into what went wrong, but said the BBC had full editorial control throughout the production of the Newsnight film.
Meanwhile, a YouGov poll for The Sun found that 44% of Britons trust the BBC’s journalists, the first time the figure has dropped below 50%.
Deputy Prime Minister Nick Clegg, asked to comment on the £450,000 payoff to Mr Entwistle, told ITV’s Daybreak: “It is difficult to justify, difficult to explain, isn’t it?
“My reaction was like everybody else’s.
“Mr Entwistle was offered this money, he did not need to take it and it is up to the BBC to justify, as Lord Patten sought to, why they took this decision.”
Speaking to BBC Breakfast, Mr Clegg said: “Mr Entwistle’s payoff is hard to justify, it is hard to explain. I guess he did not need to take it when it was offered to him.
“But it is not really for government to micro-manage these things in the BBC. The BBC is quite rightly independent of politics and of government but it is up to the BBC to seek to justify these kinds of decisions when they are made.”
Asked about calls by MPs for Lord Patten to consider his position as chairman of the BBC Trust, Mr Clegg said: “I don’t think it is the time to go round claiming that X person at the BBC should be promoted or Y person should resign.
“Clearly, the BBC is in a very difficult situation and is suffering a real crisis if you like of confidence in parts of the way in which some of the journalism is done in some programmes.
“I think everybody wants the BBC now to respond to that in a strong, robust, thorough way, so the BBC can go back to being the world class broadcaster for which it has been well known here in this country and around the world for many, many years.”