Hundreds of teachers and carers are working without completed criminal checks.
Schools have been forced to let some staff start before being investigated by the Criminal Records Bureau (CRB).
Vital checks have been delayed in a backlog at the CRB caused by new guidelines.
The Government now requires employees to have written evidence their background has been processed. That is being blamed for the slow turnaround.
West Sussex County Council advised schools to allow some teachers to start with outstanding CRB checks.
Its human resources department has waited up to three months for checks to be returned.
A council spokesman said: "With 5,000 new starters every year in our schools, there will be on very rare occasions, times when the process cannot be completed in time for a person taking up their employment.
"For example, someone taken on in the summer who may need to be in post for the start of the September term.
"In these cases our advice to schools is that they must carry out a risk assessment to decide on the level of supervision needed for someone who will be working with children prior to the completion of the CRB check."
County councils have a temporary back-up called a List 99, containing details held by the Government about people banned from working in schools.
West Sussex County Council has introduced a single database system and support staff costing £500,000 to make sure records were up to date and reliable.
No figures were available yesterday***24/4*** for the number of outstanding CRB checks on West Sussex council staff in education and social services.
East Sussex County Council is waiting for CRB checks to be completed on nearly 300 teachers.
A spokeswoman said: "There are more than 4,600 teachers employed by East Sussex County Council. When employing teachers a thorough series of checks is carried out, including references and CRB and List 99 checks.
"Ofsted shares our confidence that all appropriate checks have been completed for all staff, but highlighted that record keeping of these checks could be improved.
"Since December 2006 all individuals who did not need a CRB check have been rechecked against List 99. As anticipated, no concerns have been raised by these checks.
"In December, 294 teachers were identified as needing to be CRB checked again. This work is ongoing and we expect all records to be fully updated in the near future."
Brighton and Hove City Council is awaiting results on around 200 school staff.
A spokesman said: "New government guidelines have required schools to have written evidence of CRB checks for all staff. This meant staff for whom there was no written evidence of a check had to be re-checked. This was due to be done by the end of March.
"In most cases our schools already had the written evidence. The delays apply to around 200 staff who started after April 1 2002 where there is no physical record of a CRB check being carried out.
"All CRB re-checks were sent to the CRB on time and are being processed."
He said all the city council's schools-based staff have been cleared against the List 99.
The spokesman added: "Child protection is always our top priority and we are working with our schools to ensure that they all have watertight recording systems.
"We are confident our schoolchildren are as safe any children in the UK."
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