Some 2,700 people have been wrongly labelled as criminals by the Criminal Records Bureau (CRB), it has emerged.
The mistakes have led to some people being turned down for jobs.
The Home Office said the errors arose when personal details were similar to those of people with a conviction, but were "a tiny proportion of cases".
It said 90% of disputes were resolved within 21 days and, while errors were regrettable, it would not apologise for its "caution".
Education Secretary Alan Johnson told the BBC only 0.03% of the nine million "disclosures" the agency makes had been wrong, so the issue had to be put "into context".
Emma Budd, from Maesteg, South Wales, lost out on a job she was offered by a children's charity when she was incorrectly identified by the CRB as a convicted shoplifter.
Emma Budd was wrongly identified as a convicted shoplifter
She said: "Because they sent the CRB check to the employee and the employer at the same time, the job just went out the window.
"Then I had a letter of apology which said it wasn't their fault."
The CRB is an executive agency of the Home Office which runs checks for organisations recruiting people to work in positions of trust, often with children.
The Home Office said customer satisfaction about the checks was "now at an all-time high" and said last year's checks prevented 25,000 unsuitable people being recruited.
It said it made "no apology for erring on the side of caution".
A spokesman said: "The Criminal Records Bureau's first and foremost priority is to help protect children and vulnerable adults by assisting organisations who are recruiting people into positions of trust.
"We err on the side of caution in these rare cases precisely because it is vital to ensure that the disclosure individuals do not fraudulently try to claim they have no criminal convictions when in fact they have."
He added that individuals could see the information disclosed about them, so if there had been an error, they could dispute it.
Shadow attorney-general Dominic Grieve said there was no excuse for making mistakes.
"There should be no reason why there should be mismatches of identity," he said.
"People have identifiers and it ought to be possible to resolve that issue. Lots of people in this country share the same names."
Liberal Democrat home affairs spokesman Nick Clegg said the errors took "Home Office incompetence to new absurd levels".
He added: "This latest fiasco will erase the last bit of public confidence in the Home Office."