Ken MacQuarrie, who undertook the investigation, said the corporation's flagship news programme had failed to complete basic journalistic checks.
There was also confusion about who had the ultimate responsibility for final editorial sign-off on the story.
The Newsnight report had aired claims an unnamed senior Conservative – later revealed on social media to be Lord McAlpine, a former Thatcher-era Conservative Party treasurer – was a child abuser.
It was later revealed the claim was based on mistaken identity.
Mr MacQuarrie's report found the show's editorial management structure had been seriously weakened as a result of the editor, Peter Rippon, having to step aside after he axed an investigation into Top of the Pops presenter Jimmy Savile's paedophile activities, and the loss of his deputy.
A separate chain of command had been established for Savile-related stories, but it was unclear whether this applied to the November 2 story.
The report added: "As a consequence, there was ambiguity around who was taking the ultimate editorial responsibility for the Newsnight report."
The BBC Scotland chief added: "During the editorial decision-making process, some of the basic journalistic checks were not completed. Identification was not confirmed by photograph with the first victim. The second victim could not be traced in order to provide up-to-date corroboration."
Although legal advice was sought, no right of reply was offered to Lord McAlpine, who is considering legal action.
Victim Steve Messham, who claimed to have been abused by a senior political figure, admitted he wrongly identified his abuser and apologised.
The BBC's executive board called Newsnight's failings unacceptable and said it would "now embark on a disciplinary process where appropriate".
A BBC Trust spokeswoman said the MacQuarrie report clearly showed there were "serious failures in the normal checks and balances that the trust expects from BBC journalism".
She said these had been compounded by the extra chain of command introduced to deal with Savile-related stories.
She added: "We expect to receive regular updates on this issue from the acting director-general as he works with the utmost urgency to restore public confidence in the BBC and the integrity of its journalism."
Tim Davie, who holds the role of acting director-general after George Entwistle's resignation on Saturday, said a single chain of command for news output would be put in place again.
The board is seeking to fill a vacancy for a non-executive director of the BBC with a senior external figure with a background in overseeing journalism.
Earlier, Helen Boaden, the director of news and her deputy Stephen Mitchell stepped aside pending an internal review into how the Savile claims were handled. Meanwhile, MPs attacked Mr Entwistle's £450,000 payoff – a full year's salary – for just 54 days in the position. Culture Secretary Maria Miller said it was hard to justify, while her Labour Shadow Harriet Harman urged him to give up half.
Mr MacQuarrie, 60, a Gaelic speaker and native of Mull, has spent almost 40 years with the BBC. He oversaw shows like Chewin' The Fat, and Off The Ball as Head of Programmes in Scotland.