Barnsley, Bridgend and Derby have followed Knowsley and Hull councils by ordering schools to vet all their teachers and support staff again through the Criminal Records Bureau.
Teachers in other authorities in Yorkshire and Humberside said they were also expecting blanket checks.
The councils deny that it relates to last month's row over decisions by ministers not to ban some sex offenders from working in schools.
The Department for Education and Skills has sent two letters to authorities telling them it is unnecessary for all their staff to have new checks, which cost pound;34 each.
Chris Keates, general secretary of the NASUWT teachers' union, said the councils' decisions were "a gross over-reaction which would undermine the steps taken to restore parents' confidence in schools".
"I cannot begin to quantify the distress such measures could cause to committed and dedicated staff, the burdens this will place on schools and the impact on pupils' education if there is a delay in appointing teaching staff to vacancies," she said.
"Apart from overloading the system, the potential cost on school budgets runs into thousands of pounds."
Derby city council said it ordered its 95 maintained schools to carry out the checks because staff might not have been vetted thoroughly in the past.
A spokeswoman said: "We have not taken the decision lightly. If it upsets a few people but stops something really nasty happening to kids, then it's worth it."