BBC Director General George Entwistle has admitted that the Newsnight report implicating senior Tory MP Lord McAlpine was wrong and should not have been broadcast.
Entwistle said the report was "unacceptable" and "should have never gone out".
"We should not have put out a film that was so fundamentally wrong. What happened here was completely unacceptable," Entwistle told BBC Radio 4's Today programme.
"I have taken clear and decisive action to start to find out what happened and put things right."
BBC Scotland director Ken MacQuarrie has been ordered to produce a report on why the basic mistakes were made.
"Further action will follow from that - disciplinary if necessary," added Entwistle.
Meanwhile, the BBC issued an apology for the error in its Newsnight report and also announced an immediate halt to all Newsnight investigations.
The BBC apology on air read:
"On 2 November, Newsnight broadcast a report that looked into criticism of the North Wales Abuse Tribunal.
"The report included an interview with Steve Messham, an abuse victim who said that a senior political figure of the time had abused him.
"We broadcast Mr Messham's claim but did not identify the individual concerned. Mr Messham has tonight made a statement that makes clear he wrongly identified his abuser and has apologised.
"We also apologise unreservedly for having broadcast this report."
Newsnight had reported the claims of Steve Messham that a leading 1980 Tory politician had assaulted him at the Bryn Estyn children's home in Wrexham. He called for a re-investigation into the matter as he believed the report by Sir Ronald Waterhouse in 2000 did not cover the full scale of the truth. Messham wrongly named McAlpine when a photo was shown to him by the police as his abuser. He later apologised to McAlpine and his family.
"I certainly don't want the wrong people accused, that is also wrong. That's why I'm speaking out now and I hope people believe what I say. I am sincerely sorry," said Messham.
McAlpine, who now lives in Italy, called the claims "wholly false and seriously defamatory" and said he is planning legal action against those who linked his name to the allegations.
"If he [Messham] does think I am the man who abused him all those years ago I can only suggest that he is mistaken and that he has identified the wrong person," said McAlpine.
"It is obvious that there must be a substantial number of people who saw that I had been identified in the internet publications as this guilty man and who subsequently saw or heard the broadcasts or read the newspapers in question and reasonably inferred that the allegation of guilt in those broadcasts and newspapers attached to me."
Speaking for his client, his lawyer Andrew Reid told the BBC earlier: "We need to take a number of different actions. Firstly to try to get this taken down from the internet which is not going to be easy.
"Then we have to look at Newsnight and the way in which they behaved, the way they trailed, they made it obvious who it was, or who they alleged it was by referring people to the internet.
"And all the others who have used the internet and just let people know where to go and find the answer because they made these statements recklessly."