The UK has the largest police DNA database in the world
Ministers have been accused of building a national DNA database "by stealth" by retaining profiles of nearly 40,000 children never convicted of a crime.
The government says there are 39,095 DNA profiles of 10-18 year olds from England and Wales who were arrested but never cautioned or charged.
The Home Office said retaining DNA was a "key intelligence tool" for police fighting serious and violent crime.
The Lib Dems say the DNA of "blameless children" should not be retained.
Last month, a government-funded inquiry recommended that DNA profiles of people who had never been convicted of a crime should be removed from the database, which it said should be controlled by an independent body.
But currently samples from anyone arrested for a recordable offence and detained at a police station in England and Wales - innocent or guilty - can be kept on file indefinitely. Innocent people who volunteer to give a DNA sample during a police inquiry also have their details kept on record.
People who give samples during arrest, but are later not charged or are cleared, can apply to the chief constable to have them removed in "exceptional circumstances".
In Scotland, DNA samples taken when people are arrested must be destroyed if the individual is not charged or convicted unless they are accused of a violent or sexual crime.
Junior minister Meg Hillier confirmed on Friday that there were 349,934 DNA profiles of under-18s on the database - 87.1% of whom had been either convicted or cautioned, or had received a final warning.
She also acknowledged there were 39,095 DNA profiles of youngsters who were never cautioned or charged.
Chris Huhne, the Lib Dems' home affairs spokesman, said: "These startling figures show that the government is building a national DNA database by stealth.
"There can be no excuse for storing the DNA of innocent adults, let alone children, who are entirely blameless."
He said many people with criminal records were not on the database and said the government could not be trusted with its security.
For the Conservatives, shadow home secretary Dominic Grieve said there should be a Parliamentary debate on the issue, and the DNA database should be put on a statutory basis.
"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," he said.
The Home Office argues that the database has revolutionised the way the police protect the public and is a key instrument in the fight against violent crime, burglaries and rape.
It says that in a 12-month period between 2006 and 2007, DNA evidence was used in police investigations into 644 rapes, 222 other sexual offences, 1,900 violent crimes and more than 8,500 domestic burglaries.
A Home Office spokeswoman said the government had no plans to introduce a universal database.
She added: "Inclusion on the DNA database does not signify a criminal record and there is no personal cost or material disadvantage to the individual simply by being on it."
The UK has the largest police DNA database in the world, with more than four million people on file, and it has been used to solve a number of "cold case" inquiries in recent years.