Opposition parties said it was evidence the Government was building a national DNA database by stealth and called for a parliamentary debate.
Ms Hillier was responding to a parliamentary question from Tory Grant Shapps (Welwyn Hatfield).
She said figures obtained from the National DNA Database and Police National Computer in April showed there were 349,934 DNA profiles relating to under-18s, equivalent to around 303,393 individuals because of 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.
“These startling figures show that the Government is building a national DNA database by stealth,” he said.
“There can be no excuse for storing the DNA of innocent adults, let alone children, who are entirely blameless.”
Shadow Home Secretary Dominic Grieve echoed the concerns. “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.
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.
At present, people who agree to have their samples put on the database cannot have their details removed.