The samples will be deleted from the national DNA database, but the details could be kept by local forensic science labs, it has emerged.
The Home Office says the material will be anonymised to protect people's privacy.
But civil liberties campaigners accused the coalition of a U-turn.
In a letter a committee of MPs, reported by The Daily Telegraph, Home Office minister James Brokenshire, confirmed that DNA profiles of those arrested but never charged or found guilty of a crime could still be retained by forensic scientists.
Profiles would "be considered to have been deleted even though the DNA profile record, minus the identification information, will still exist," the letter says.
'Pointless gesture' A Home Office spokesman denied the government had done a U-turn on a key coalition agreement pledge.
He told BBC News: "Our position has not changed. We will retain the DNA of the guilty not the innocent. That means the DNA records of the innocent will come off the database and physical samples will be deleted."
He confirmed that DNA samples of innocent people would be kept by forensic science laboratories because they are stored in "batches" with the DNA of guilty people making destruction of them difficult.But Daniel Hamilton, director of the civil liberties group Big Brother Watch, said the anonymised samples would still have a bar code on them which would allow them to be "married up" with information about individuals.
"The information will still be held by the state and won't be deleted, which represents a U-turn by the government," he told BBC News.
"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".
New watchdog Former shadow home secretary David Davis - a longstanding campaigner for innocent people's DNA to be destroyed - is understood to be "sceptical" about the government's claim that the DNA records of the innocent have to be retained in order to keep the records of the guilty.
But he is expected to seek a briefing from the minister before commenting further.
In last year's coalition agreement, the Conservative/Lib Dem government pledged to "adopt the protections of the Scottish model for the DNA database".
In Scotland, the DNA of convicted serious criminals is held indefinitely. Adults not convicted of a serious crime have their DNA retained for three years, with a possible two-year extension - but samples are not retained of innocent people or those convicted of minor crimes.
At the moment, the DNA of anyone who has been arrested in England, Wales and Northern Ireland is held indefinitely on a national database.
Under the coalition's Protection of Freedoms Bill, any adult convicted of a crime, or child convicted of a serious crime, will still have their DNA profile stored indefinitely in the national database.
And police will have the power to retain the DNA samples of anyone arrested for any offence, even if there is no conviction, where the individual is suspected of involvement in terrorism.
The government says its will create a new watchdog, the Commissioner for the Retention and Use of Biometric Material, to oversee and possibly reject applications to retain DNA profiles on national security grounds.
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