The BBC Trust found that, although Lord McAlpine denied the allegations when he was contacted by a Channel 4 News journalist before Newsnight was broadcast, the BBC still made no attempt to contact the peer, which it should have done.
Trustees also said that concerns had been raised previously about the credibility of some of Mr Messham's evidence - which was known to members of BBC Wales, but no effort was made to contact them.
The Trustees considered that parts of BBC News not contacting colleagues in the nations and regions when investigating stories on their patch was very poor practice.
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Counting will begin on Saturday morning, with the result expected later in the day.