The National Assessment Agency wants schools to rectify errors themselves and says they will be charged for marking reviews which do not result in an overall level change for a subject.
But the corrections made by schools will not be added to official statistics, and this could have an impact on value-added scores and local authority and Ofsted judgements on schools.
Mick Brookes, general secretary of the National Association of Head Teachers, has told the Government that the policy will lead to inaccurate value-added scores used to compile official summaries of school performance and league tables. "This affects the credibility of the school and causes extreme stress for our members," he said in a letter to Jim Knight, the schools minister.
Heads say marking errors - which may not make a difference to overall levels pupils achieve in English - are dramatically altering individual results for reading and writing, used by Ofsted and councils to assess school performance.
Inspectors raised pupil attainment in English writing tests in their last report on Sandwich junior school, in Kent.
Gary Rees, the head, had expected a marked improvement this year but was disappointed to discover that only 22, or 47 per cent, of pupils reached the expected level 4 in writing. When he examined the papers, he found marking errors in all 49, which if rectified, would have boosted the total to 36, or 73 per cent of the cohort. But because the overall levels for only four pupils for English would have been changed, he is unable to get the marks reviewed.
"What they are saying is that levels for reading and writing don't matter, but they do," he said. "I suspect this is a cost cutting exercise. "We think we have had a bad marker. To be told we can't appeal against this is a real kick in the teeth.
"Surely the job of an external marking agency is to ensure accurate, impartial assessment. To then say that schools correct the marking themselves is an abdication of responsibility."
A Department for Education and Skills spokeswoman said the impact of schools amending their own marks was being evaluated as part of a pilot on contextual value-added scores.
She said there was a system in place to allow schools to tell inspectors about any revisions to marks that they felt should be taken into account.