The BBC has begun disciplinary proceedings against its own staff after admitting that “basic journalistic checks were not carried out” by its flagship programme Newsnight where “unacceptable failings” in editorial procedures led to the Tory grandee Lord McAlpine being falsely linked to a paedophile ring.

Publishing the summary findings of an internal inquiry into the flawed report, which prompted the resignation of the BBC Director General George Entwistle on Saturday, the BBC said that it was taking “clear and decisive action” to “restore public trust in the BBC’s journalism”.

In his first move as acting Director General Tim Davie set up a new editorial “clear line of command” and side-lined the two most senior figures in the BBC News division, Helen Boaden and Stephen Mitchell. Both executives were understood to have brought in lawyers to oppose the development.

Responding to the internal report compiled by Ken MacQuarrie, the director of BBC Scotland, into the Newsnight programme the BBC said it needed to take “immediate” action to address “the lack of clarity around the senior editorial chain of command”.

As Mr Davie announced his intention to offer “strong leadership” to the beleaguered organisation, the National Audit Office announced that it would be asking the BBC Trust to explain its decision to pay £450,000 to Mr Entwistle.

Mr Davie, who expressed a wish to talk to Lord McAlpine “personally” about the story. He said the report highlighted “a degree of complexity in news operations which led to some fuzzy decision-making”. He promised that individuals identified in the report as being culpable for the editorial failings would be subject to a “disciplinary process” that would be “fair to those individuals”.

But as those proceedings began there was a fear of scapegoating among BBC staff.

Newsnight staff fear that the programme is to be closed down and a number of them issued a statement through the National Union of Journalists saying they were “appalled at what happened, and that the overwhelming majority of those who work there had no involvement with the story, and were not consulted about it before broadcast”.

Several members of the Newsnight team are taking legal advice in addition to the programme’s editor Peter Rippon who has instructed lawyers after being side lined by the BBC after posting a blog about his reasons for not running an investigation into allegations of child abuse by Jimmy Savile.

The Corporation confirmed yesterday that the Newsnight investigation that suggested a senior Tory was implicated in child abuse had been referred to Peter Johnston, the Northern Ireland controller and a BBC management board member, before being shown.

In explaining his decision to move Ms Boaden and Mr Mitchell, Mr Davie said that he wanted to show he had a “full grip of the situation”. He said: “I have to be, as Director General, very clear on who is running the news operation.” But the BBC’s business editor Robert Peston reported that lawyers acting for Ms Boaden and Mr Mitchell had argued that they were “quite capable” of running BBC News even while the Pollard inquiry into the Savile investigation was ongoing. The lawyers are likely to be from the BBC legal department and both executives hope to return to their jobs.

Rob Wilson, the MP for Reading East, warned that the BBC could be facing a “slow motion car crash” of legal battles. “It does seem quite extraordinary that the BBC is apparently paying for its own staff to sue itself. I don’t know what was behind Boaden and Mitchell being moved aside today, but it appears it may have backfired. The BBC ship still appears worryingly rudderless.”

Steven Barnett, Professor of Communications at the University of Westminster, said: “There’s a danger of this spiralling into a litigation battle. Everyone says we are expecting heads to roll without any consideration for the individuals who might have been caught up in this but have been doing their job properly.”

The full MacQuarrie report will be “used to inform disciplinary proceedings”, the BBC said. The summary report said that Newsnight’s editorial management structure “had been seriously weakened” since the decision to move Mr Rippon. “The editorial leadership of the team was under very considerable pressure”.

It also highlighted the “lack of clarity” in the BBC’s editorial chain of command and said that “it was not clear whether this story was regarded as Savile-related or not”. Both Ms Boaden and Mr Mitchell had been stood aside from responsibility for the McAlpine piece because they were connected to the internal inquiry into why Newsnight had not broadcast evidence about Jimmy Savile.

In the House of Commons, Mr Entwistle’s severance payment was the subject of heated criticism. Under his contract, the departing Director General was entitled to only six months' salary, but the BBC Trust said the extra payment had been agreed to reflect Mr Entwistle’s continuing involvement with the internal inquiries set up following the exposure of Jimmy Savile’s activities.

Lord Patten, its chairman, has insisted the golden goodbye was justified although he said that if Mr Entwistle had not resigned the BBC Trust would have had to consider “the option of termination”.

During an emergency Commons debate, several Conservative MPs called for Lord Patten to step down as chairman of the BBC Trust. Philip Davies said the BBC chairman had been “asleep at the wheel” and “off the pace from the word go”. They were supported by the Labour MP John Mann who told the Commons: “How can the BBC move on unless and until Lord Patten is sacked?”

But the Government made clear it had confidence in Lord Patten and the Culture Secretary, Maria Miller said the corporation needed a “period of stability” to see it through the current turmoil. “Lord Patten has a key role in making sure this crisis is now well handled and I support him in now doing that.”

The Prime Minister and Maria Miller also criticised the £450,000 pay-off given to George Entwistle, calling it "hard to justify", as the BBC saw senior news staff sidelined in the ongoing crisis.