Council leaders predict children will be sent home because there will not be enough staff and that it could take until Christmas before the backlog of checks is cleared.
Graham Lane, education chair of the Local Government Association, expects thousands of teachers to be turned away at the start of term. "That is a fact, not an opinion," he said.
Education Secretary Estelle Morris ordered a rethink of vetting procedures on staff working with children following the murders of Holly Wells and Jessica Chapman.
The Criminal Records Bureau, set up to provide checks for schools and other employers, has redeployed 100 staff to help deal with a backlog that has built up since it opened last April.
The number of applicants on the waiting list of prospective teachers has dropped from 22,000 last Friday to 18,000 on Monday, and the Home Office is optimistic all will be vetted by the time term starts.
However, at the current rate of progress the backlog is predicted to be at least 6,700 on the September 4 deadline.
Schools had previously been allowed to employ teachers before all the checks had been made, providing they did not appear on List 99, the dossier of people who should not work with children. Now both sets of checks must be completed before a teacher is allowed to set foot in a classroom.
South Tyneside had planned to send teachers into schools next term before the full checks were completed and inform heads if problems were later revealed. A spokesman said the authority was now uncertain if all teachers would be checked in time.
City Technology College in Wandsworth, south London, was planning to open to all 1,000 of its pupils today until principal David Durban realised 12 newly-qualified teachers had not been completely cleared. Parents have been told to keep their children off for three days.