The national DNA database contains the profiles of almost 40,000 innocent children, the Home Office said today.
Junior minister Meg Hillier said the profiles of an estimated 39,095 10 to 17-year-olds who "had not been convicted, cautioned, received a final warning/reprimand and had no charge pending against them" were on the database.
Opposition parties said it was evidence the Government was building a national DNA database by stealth and called for a parliamentary debate on the issue.
Ms Hillier was responding to a parliamentary question from Tory Grant Shapps (Welwyn Hatfield).
She said figures obtained from the National DNA Database (NDNAD) and Police National Computer (PNC) in April showed there were 349,934 DNA profiles relating to under-18s, equivalent to around 303,393 individuals due to replication rates.
"Of those estimated 303,393 persons, 264,297 (87.1 per cent) had a conviction, caution, reprimand or had received a final warning," she said.
"And 39,095 (12.8 per cent) had not been convicted, cautioned, received a final warning/reprimand and had no charge pending against them."
Liberal Democrat home affairs spokesman Chris Huhne said it was wrong to store the DNA of innocent people and argued there were serious shortcomings when it came to convicted criminals.
"These startling figures show that the Government is building a national DNA database by stealth," Mr Huhne said.
"There can be no excuse for storing the DNA of innocent adults, let alone children, who are entirely blameless.
"This is an intrusive policy that gives far too much sensitive information to the state, when we know that ministers cannot be trusted with its security.
"The DNA that should be on the database is that of past offenders, yet when it comes to them, there are major gaps in the database."
Shadow home secretary Dominic Grieve echoed the concerns about prisoners.
"This is yet more evidence that the DNA database is totally arbitrary with tens of thousands of innocent kids on it but not every offender in our prisons," Mr Grieve said.
"This is why we need to have a parliamentary debate on the issue and to put this database on to a statutory basis."
Last month a Government-appointed advisory body said there should be a more straightforward system for innocent people to have their samples removed from the database.
The Ethics Group said samples obtained during police investigations should be destroyed at the end of an inquiry rather than loaded on to the NDNAD.
At present, people who voluntarily agree to have their samples put on the database cannot have their details removed.
Suspects who give samples after being arrested but who are later either not charged or cleared can apply to the Chief Constable who can agree to remove the listing in "exceptional circumstances".
The Ethics Group said this was "potentially inconsistent and discriminatory and contrary to an individual's privacy rights".
A Government-funded inquiry also said innocent people should have their profiles deleted from the database, arguing that even guilty people who have served their time should eventually have their DNA records erased because retaining the profile "continues to criminalise them".