Home secretary Jacqui Smith said the Home Office would take "immediate steps" to ensure the DNA of children under the criminal age of responsibility is taken off the database.
But she said under-18s would continue to be added to the database, under guidance to be published next year.
She said: "There's a big difference between a 12-year-old having their DNA taken for a minor misdemeanour and a 17-year-old convicted of a violent offence, and next year I will set out in a white paper on forensics how we ensure that that difference is captured in the arrangements for DNA retention."
The government intends to consult on making the system flexible for young people. "That may mean letting the 12-year-old I mentioned come off the database once they reach adulthood," said Smith.
The announcement follows the European Court of Human Rights ruling earlier this month, which stated that an 11-year-old from Sheffield had his privacy rights breached when police retained his DNA sample after he was acquitted of attempted robbery.
Home Office estimates indicate that the police currently hold DNA profiles of up to 360,000 children.
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