Many secondary schools have plummeted down league tables after the ministers raised the bar for expected achievement.
The school ranks highly on the progress pupils make
Schools are now judged on how many pupils achieve a good set of GCSE passes including English and maths.
Before, the measure was good grades in any five GCSEs (A* to C).
The change has been a blow to Grange Secondary School in Oldham, Lancashire, which has a high proportion of children who do not speak English at home.
The school ranks high on the new contextual value-added measure, meaning that pupils who go there achieve more than similar children at other schools.
But it has dropped down from a position near the top of the local league table - when all GCSEs were counted - to the bottom.
While 69% of pupils passed five GCSEs at good grades this year, only 15% managed to get five good GCSE passes including English and maths.
Across England, 46% of pupils achieved five good GCSEs including England and maths, while about 59% passed five GCSEs of any subject at good grades.
Ministers insist it is right to give parents a fuller picture of a school's achievement and to expose schools which do not do well in English and maths.
But secondaries - such as Grange School - which serve many very deprived children who struggle with English - say this should be taken into account.
Grange's head teacher Graeme Hollinshead, said: "Our pupils are coming to our school with levels in English and maths which are lower than the national average.
"It takes some of them a bit longer to get to the level of C or above."