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
Oliver Letwin MP, who was in charge of Brexit negotiations for two weeks, tells ITV News what he thinks will be easy and what will be hard.
Theresa May's decision to delay green-lighting Hinkley nuclear plant has put noses out of joint. But EDF is confident it will go ahead.
Highs of 23C at best in the afternoon sunshine but feeling cooler in the mornings and the evenings.