This has meant that the police?s national DNA database holds more than five million profiles, including one million people with no criminal conviction.
Experts say storing the DNA of innocent people gave them an unfair ?presumption of guilt? in the eyes of the police.
The Coalition agreement last May said the Government would ?adopt the protections of the Scottish model for the DNA database?.
DNA samples from innocent people would be deleted, apart from those accused of a sexual or violent offences, which would be held for five years.
However, Home Office minister James Brokenshire admitted to MPs on a committee which is considering the legislation that police forces will retain innocent profiles.
Mr Brokenshire said he had won agreement from the information watchdog that the DNA profiles could be retained by forensic science laboratories.
This would mean that the profiles would ?be considered to have been deleted (even though the DNA profile record, minus the identification information, will still exist)?.
However Mr Brokenshire admitted that it would be still be possible to identify the anonymised profiles.
He said: ?Members of the committee will be aware that most DNA records ? will include the original barcode, which is used by both the police and the FSS [Forensic Science Service] to track the sample and resulting profile through the system.
?It is therefore theoretically possible that a laboratory could identify an individual?s profile from the barcode, but only in conjunction with the force which took the original sample, by giving details of the barcode of the force and asking for the individual?s name.?
This would be a ?would breach the Data Protection Act, and would not be accepted as evidence in a criminal investigation?, he said.
However civil liberties groups were outraged by the apparent about-turn.
Isabella Sankey, policy director at Liberty, told The Daily Telegraph: ?Anonymising intimate genetic information is nowhere near the same thing as destroying it, and this letter represents a massive U-turn on the part of two parties who promised that innocent people?s DNA would be destroyed.?
Retaining the profiles was a breach of a ruling by the European Court of Human Rights which ruled in 2008 that it was unlawful.
She added: ?This breach of promise is also in breach of the judgment of the Court of Human Rights and more litigation will no doubt follow.
?The minister?s assurance that criminal offences under the Data Protection Act are sufficient safeguard against DNA being re-identified is like saying that phone-hacking offences protected people?s privacy from the News of the World.?
Daniel Hamilton, a director at campaign group Big Brother Watch, said: ?This is a disgraceful U-turn on the part of the government. Destroying physical DNA samples is a pointless gesture if the computer records are to be retained.
?Despite paying lip service to freedom and civil liberties, this government is fast proving itself to be every bit as illiberal as its predecessor.?
Unveiling the legislation in January, Mr Clegg, the deputy Prime Minister, said the new Bill would ?end the indefinite storage of innocent people?s DNA?.
The measure was also backed by Prime Minister David Cameron when he was in Opposition. In a speech in June 2009, he said: ?Nearly five million people are on Labour?s DNA database.
?The Government says it?s to help fight crime. But almost a million of the people on it are completely innocent. And tens of thousands of those innocent people are children.
?It?s a situation that would cause concern under the most oppressive regimes in the world, but it's happening right here, right now in Britain... And we will remove innocent people's records from the DNA database.?
Last year, Sir Alec Jeffreys, the pioneer of genetic finger-printing, warned that keeping innocent people's DNA on the national database causes such distress it drove one man to kill himself.
He said storing the DNA of innocent people gave them an unfair "presumption of guilt" in the eyes of the police.
A Home Office spokesman insisted that profiles would be completely deleted from the national DNA database.
However within individual police systems, profiles are recorded in batches and it was not possible to delete one without affecting the rest, including convicted offenders.
The spokesman said: ?Our position has not changed at all. We will retain the DNA of the guilty, not the innocent.
?That means DNA records of the innocent will come off the database and physical samples will be deleted.?
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