Schools have been told they can take on staff who have not been cleared by the Criminal Records Bureau, as long as checks on the Government's List 99 - a dossier of people banned from working with children - are carried out.
Estelle Morris said she was letting staff work after a "fast-track" check because the bureau's failure to do full checks before the start of term was causing chaos.
The Education Secretary added: "My whole concern is for the well-being of pupils. I could not allow the disruption to our schools to continue ... It is our firm intention to bring in the full CRB check when the system is able to cope."
Later, speaking on Channel 4 News, she apologised for any role she had in bringing the chaos about.
She said she had reached her decision after discussions with the teacher unions, employers and Home Secretary David Blunkett, whose department oversees the bureau. He assured her education staff checks remain a priority.
Fast-track checks were abandoned after the deaths of Jessica Chapman and Holly Wells. The Department for Education and Skills said all staff working with children should receive full vetting. Ian Huntley, a school caretaker, has been charged over the deaths.
But with thousands of checks outstanding, children were sent home in areas including London, Leicestershire, Surrey, the West Midlands, Greater Manchester. North Yorkshire, Gloucestershire. Even before Ms Morris's U-turn, at least four London boroughs had been letting teachers whose checks were still pending take lessons.
The Secondary Heads Association, the National Association of Head Teachers, and the Local Government Association are urging the Government to compensate schools for money already spent on supply staff.
The cost works out at around pound;750,000 a day, although some schools had not been able to get supply teachers because they too were waiting to be vetted. John Dunford, general secretary of the SHA, said: "Schools'
supply budgets are big enough without the Government adding to them."
LGA education chairman Graham Lane has warned of more difficulties later this term when schools need to check new governors and might find other non-teaching staff had not been cleared.
Cheshire has already cancelled some school buses because of difficulties finding "cleared" drivers.
Safer Recruitment, a firm that has processed more than 100 applications for checks to the CRB, said only its private-school clients had so far asked for support staff checks.
The Home Office said claims would be considered if they were based on proven error at the CRB. Compensation was unlikely where clearance had simply been delayed.