Secondary schools will get extra points for their English and maths exam results in a new league table this summer, a change that officials admit will make struggling schools look worse.
The change is being made to the contextual value added (CVA) measure, which is based on GCSE results. It was originally designed to give schools with low-performing pupils proper credit because it took factors beyond teachers' control, such as pupil background and prior attainment, into account.
But a government document seen by The TES shows the reformed measure will push most secondaries with low, unadjusted, raw GCSE results down the CVA league table. It also admits the measure will "further penalise pupils with low scores".
Ministers have already been criticised for their National Challenge scheme, which threatened hundreds of schools with closure because of low raw GCSE results, but did not take pupil background and Ofsted verdicts into account.
Angry heads say the change is the "final straw" and could lead to an exodus of talented staff from schools in tough areas where they are most needed.
CVA is based on an average points score per pupil for their best eight GCSEs or equivalent, adjusted to take account of factors such as ethnicity, gender, deprivation and previous exam results.
From this summer, CVA point scores will be boosted by every English and maths qualification - on a sliding scale, according to the grade and type of qualification.
The Department for Children Schools and Families (DCSF) document includes a graph showing that most secondaries where fewer than half of pupils gain five A*-C GCSEs including English and maths will end up with lower CVA scores than before as a result of the change. In most schools where more than half of pupils reach the benchmark for raw GCSE results, CVA scores will be boosted.
Mo Laycock, head of Firth Park Community Arts College, Sheffield - where 26 per cent of pupils gained five A*-C GCSEs including English and maths - has calculated the change will mean a drop in CVA from 1,020 to about 1,000.
She and other heads in schools serving disadvantaged areas believe it is unfair and will damage morale.
"We are not magicians," Ms Laycock said. "If children come in with massive literacy issues, it is so much harder to get them up there.
"Why can't we be celebrated for what we do? Staff work hard here because they believe in these kids. But if the Government ups the ante like this, then these dedicated teachers will start to leave for schools where the job is less onerous."
DCSF figures show the change will mean a rise in the number of National Challenge schools with CVA significantly below the national average, and a drop in the number of those in the scheme with CVA scores significantly above.
Mary Bousted, Association of Teachers and Lecturers general secretary, said the change seemed muddled and counterproductive.
A DCSF spokesman said low-performing schools would not necessarily suffer from the new measure. "Low-attaining schools that channel their efforts into progressing young people in English and maths are likely to do very well," he said.