A BBC Newsnight report in which an abuse victim accused an ex-Tory politician of sex abuse should not have been broadcast, BBC director general George Entwistle says.
He apologised unreservedly to Lord McAlpine after the report led to him being wrongly implicated in abuse at Welsh care homes.
Mr Entwistle said he was only aware of the episode after it was broadcast.
The BBC Trust said it expected "appropriate action" to be taken.
Lord McAlpine, although not named on Newsnight, was wrongly identified on the internet as the alleged abuser.
The abuse victim, Steve Messham, apologised to Lord McAlpine, a former Tory treasurer during Margaret Thatcher's leadership, after saying he did not assault him.
Mr Messham said in the 1990s he was shown a photograph by police of his alleged abuser but was incorrectly told it was Lord McAlpine. On Friday, he was shown another photo - and realised it was not the peer.
Newsnight had reported on 2 November Mr Messham's claims against a leading 1980s Tory politician without naming him.
Mr Entwistle said: "It's no kind of excuse or exoneration, but it's important to say that the film itself did not make a named allegation".
Mr Entwistle, speaking on BBC Radio 4's Today programme a day after the apology, said: "We should not have put out a film that was so fundamentally wrong. What happened here is so totally unacceptable. In my view the film should not have gone out".
He has commissioned a report from BBC Scotland director Ken MacQuarrie into what happened with the Newsnight investigation, and expects to see it on Sunday.
"This was a piece of journalism referred to senior figures within News, referred up to the level of the management board and had appropriate attention from the lawyers," Mr Entwistle said.
"The question is, in spite of all that, why did it go wrong? Something definitely went wrong, something definitely and clearly and unambiguously went wrong."
Asked if he should have been aware of it as he is the editor-in-chief, he said "not every piece of journalism made inside the BBC is referred to the editor-in-chief".
Earlier, Lord McAlpine said the claims were "wholly false and seriously defamatory".
His solicitor, Andrew Reid, said the peer will take legal action against those who later named and linked him to the false allegations.
As well as the report from Mr MacQuarrie, the BBC ordered the following:
- A senior news executive was sent to "supervise" Friday night's edition of Newsnight
- An apology was broadcast on Friday's programme
- An "immediate pause in all Newsnight investigations to assess editorial robustness and supervision"
- An "immediate suspension" of all co-productions with the Bureau of Investigative Journalism which Newsnight worked with on the programme
Mr Entwistle said questions needed to be asked about the Newsnight film: "Did the journalists carry out basic checks, did they show Mr Messham the picture, did they put allegations to the individual, did they think of putting allegations to the individual, if they did not, why not, and did they have any corroboration of any kind?".
If necessary, disciplinary action would be taken, he said.
The BBC Trust, the corporation's governing body, issued a statement on Saturday, saying "this is a deeply troubling episode".
"The Trust notes the BBC Executive's apology and would like to offer its own apology also. The Trust has impressed upon the DG the need to get to the bottom of this as a matter of the utmost urgency and will expect appropriate action to be taken as quickly as possible."
Newsnight is already under investigation for its reporting of abuse by former BBC presenter Jimmy Savile.
However, Mr Entwistle said there was no suggestion the programme would be shut down, saying such a move at this stage would be "disproportionate".
He also said the BBC was suffering a "bad crisis of trust", but emphasised it surrounded Newsnight, not other output by the corporation.
"It's very important to recognise that this is about Newsnight. Of course this has huge implications for the BBC, for trust in the BBC, but it would be absolutely wrong to slur by extension the rest of the amazing work going on across BBC News. Ninety-nine per cent of what the BBC does is going out to the usual excellent standards."
Questioned about his own position, Mr Entwistle, who became director general in September, said he answered to the BBC Trust.
"I am doing the right things to try and put this stuff straight. I am accountable to the Trust in that endeavour. If they do not feel I am doing the right things, then obviously I will be bound by their judgment."
Culture Secretary Maria Miller said the "BBC Trust needs to get to the bottom, and quickly, of what has gone wrong at the corporation.
She added: "The events of the last few days only serve to underline the vital importance of restoring credibility."
Meanwhile, shadow culture secretary Harriet Harman said "something has gone badly wrong at Newsnight".
She said: "The director general only took over the leadership of the BBC eight weeks ago, but he needs to show decisively that he is addressing the systemic problems which are in evidence here."
MP John Whittingdale, chairman of the culture, media and sport select committee, said the BBC "needs to act very swiftly in order to try to restore some public confidence".
The director general is expected to attend a committee session in Parliament, alongside BBC Trust chairman Lord Patten, near the end of November, and Mr Whittingdale said he will consider bringing this forward.
Labour's Ben Bradshaw, a former culture secretary and another member of the committee, said Mr Entwistle had to "get a grip".
He said "it certainly feels from the outside that BBC News management is now totally dysfunctional" although he did not believe that Mr Entwistle should stand down.
Kevin Marsh, a former editor of the Today programme, said Mr Entwistle did not give the impression of "a man who is absolutely in charge of everything".
"He can survive it but I think he's made it very difficult for himself."