The report from the BBC Trust's Editorial and Standards Committee said the failure by Newsnight was "extremely concerning".
It found that the freelance reporter Angus Stickler, who brought the story to Newsnight, was considered a "safe pair of hands" and may have been subjected to "lighter-touch editorial checks" than if he had been less well-known to the BBC.
It said the report was wrongly treated as if it had two sources, Steve Messham, and an interview with a second victim broadcast on BBC Five Live in 2000, who could not be contacted during the making of Newsnight.
The Trustees agreed that members of the Newsnight team were wrong to regard this as a report with two sources, given that the second witness could not be found.
The Trustees found it particularly concerning that, at no point in advance of the broadcast of the Newsnight report, was Mr Messham shown a photograph of Lord McAlpine and asked to confirm that he was the individual at the centre of the allegations.
More top news
Donald Trump's revised immigration ban targets the same seven Muslim majority countries listed in his original executive order, sources say.
People convicted of cruelty against animals should face much harsher prison sentences, some charities have claimed.
Theresa May has been warned by EU ministers that Britain's Brexit negotiators must be prepared to compromise or risk a "crash landing".