During the trial of a man who was accused of breaking into the home of television presenter and journalist Dr Miriam Stoppard, it emerged that supposedly matching prints were "fatally flawed".
South Yorkshire police have been asked to investigate the case, which involves an expert from the Metropolitan Police's fingerprint bureau. Dozens of previous convictions in which fingerprint evidence was used are being re-examined. If fundamental errors are uncovered, it may lead to a flood of appeals.
Positive matches of fingerprints are considered flaw-proof and Scotland Yard said that this was the first time a false reading had been provided in a trial during the bureau's 96-year history.
The controversy arose from the trial of Andrew Chiori, 21, who was accused of breaking into Dr Stoppard's west London home in 1995 and stealing pounds 41,000 worth of valuables.
Southwark Crown Court heard that Scotland Yard finger print expert Simon Harris was "in no doubt" Mr Chiori was responsible after examining prints found at the crime scene. But experts called by Mr Chiori's legal team said Mr Harris's conclusions were "fatally flawed".
Mr Chiori was formally acquitted yesterday after Peter Grieves-Smith, prosecuting, conceded Mr Harris made "an error of judgement". Mr Chiori spent two months in jail on remand before being released.
Mr Grieves-Smith told Judge Butler: "I am asked to apologise for the error that he made. The work he has done in the past is being double-checked".
Judge Butler replied: "He simply got it wrong? Well, we all make mistakes. But he'll have to explain it to the inquiry.
"But there is no doubt thrown on the ethicacy of fingerprint evidence being used for the prosecution, provided the expert does his work properly," he added.
Detective Superintendent David Foss, of South Yorkshire Police, has been asked to investigate the case. A Scotland Yard spokeswoman said it was a "human error". "It's the first time this has happened at the Metropolitan Police fingerprint bureau."
The issue of fingerprint evidence was raised last November when some of Britain's leading forensic experts accused chief constables of scrapping the standard of proof for fingerprint matches to boost convictions. Fingerprint specialists at Scotland Yard told The Independent they were angry that police chiefs have decided the current 16-point match standard is unnecessarily tough and results in guilty people going free.
The Association of Chief Police Officers (Acpo) has agreed to drop the existing standard in favour of one used in Australia in which the prosecution relies upon a qualified expert to determine whether two sets of prints match.
But the Veteran Fingerprint Experts' Association, which is made up of civilian specialists in the Metropolitan Police, who have at least 25 years experience, believes the changes could result in miscarriages of justice.
Peter Jones, chairman of the Expert's Association, said: "As soon as you start tinkering with the standard, there's a chance you could get it wrong."