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
The family of a wealthy British man has claimed he was murdered by his Ukrainian bride in Kiev so she could inherit his fortune.
Medics and flight crew had been rescuing an injured skier when they crashed in the region of Abruzzo.
A story of two halves