A measure designed to promote inclusion is actually penalising some schools with large numbers of children with special needs.
Schools which have many pupils with particularly severe learning difficulties are being unfairly treated under the contextual value added measure, which is a key element in Ofsted verdicts, headteachers said.
Contextual value added (CVA) scores are supposed to show pupil progression. They take into account such factors as ethnicity, deprivation and whether English is a first language.
They also identify children as either having a statement of special needs or not, and then compare the progress they make against all such pupils nationally.
But Nigel Utton, head of St Lawrence CofE Primary School at Alton, Hampshire, said it was unfair to expect schools with many children with severe special needs to achieve the same progress as those educating large numbers with milder difficulties.
He found his school's contextual value added score rose when he took out the results of two pupils who have severe special needs using the Government's statistical tool, Raise Online.
Mr Utton, who is chair of Heading for Inclusion, said that judging schools on outcomes - whether raw scores or CVA - was not the best way to promote inclusion. He said: "I have one boy who will not make two levels between year 2 and year 6 and it would be silly to expect him to. The scores are set as statistical averages, but these are children who are outside statistical averages.
"Their needs are so very, very different. A child can have a statement for being one year behind his peers, or five years behind. But this system treats both of them the same."
A spokeswoman for the Department for Schools Children and Families said: "It is wrong to look at this on an individual basis, as removing one pupil can of course raise the CVA level if that pupil has not progressed well. But removing another pupil with SEN could send a school's CVA score down. It all depends on that particular pupil.
"It is wrong to say that overall SEN pupils bring down schools' CVA, as SEN pupils will have a mean CVA score that is neutral and does not pull down or push up the overall picture."
The inclusion of contextual scores has already highlighted contradictions in the way schools are judged. In secondaries, around 40 per cent of schools deemed to be "failing" because they have fewer than 30 per cent of pupils achieving five good GCSEs including English and maths, have CVA scores that show their pupils are making above average progress.