Schools in Bradford reopened today to find that a "significant" number of new members of staff have not been passed fit to work with children.
Delays at the new Criminal Records Bureau mean teachers and other staff in Bradford are still waiting to be vetted.
Education Bradford, which believed last week that the district would escape the crisis, was forced to issue a new statement last night admitting there were problems.
A number of Bradford schools are due back today although others are not starting until tomorrow, Friday or Monday.
A handful of schools across the country opted not to open because of the numbers of teachers waiting for clearance.
Others have taken a pragmatic approach and reorganised lessons, brought in vetted supply teachers or placed another adult in classes where staff had still to receive clearance from the CRB to ensure they are never alone with children.
A spokesman for Education Bradford said any decisions on whether or not to open schools as usual was being taken by head teachers and governing bodies, but had to be authorised by director of education Phil Green.
"Although there are still a small number of completed checks coming through the CRB, there are a significant number of outstanding clearances," he said.
"Education Bradford has done everything asked of it, but, despite continual assurances from the CRB over the last week, it now looks as if there could be difficulties for some schools at the start of the new school term.
"We will continue to do all we can to support schools dealing with problems which might arise."
Bob O'Hagan, head teacher at Rhodesway School which has taken on 48 new members of staff this year, said he had not encountered any problems.
He said: "The Government eased the rules on Monday and said certain groups didn't have to have fresh checks before the start of term, if they had had them done previously. Anyone who has come direct from another school will have had them, and newly-qualified teachers have them done at the beginning of their NQT year."
He said he believed schools would find ways to work round the problem, perhaps by placing another adult such as a school secretary in the classroom alongside a new member of staff who had not yet received clearance.
Stuart Herdson, of the Bradford branch of the Association of Teachers and Lecturers (ATL) union, said he agreed with this approach.
"It is better to have children in school and supervised rather than at home and unsupervised, or out on the streets," he said.
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