NANTWICH headteacher Philip Roy fears primary schools may stop taking in special needs pupils because of the effect of performance tables.
The Government published the Key Stage 2 tables this week and many schools in Crewe, Nantwich and Sandbach scored 70 per cent and above in the tests in English, Maths and Science.
But other schools including Wyche Primary scored low marks which headteacher Philip Roy believes is due to the way the tables are calculated.
The number of special needs pupils at the school either in separate classes or integrated into the mainstream are not taken into account.
Mr Roy and headteachers at several Crewe schools including Leighton Park, Hungerford and Church Coppenhall in Crewe are calling for changes to the system.
"You need to take into account the schools that have special classes for children and those which are integrating them into the main stream classes," said Mr Roy.
"For these children the tests are inappropriate but they still get tested and marked down as failures.
"What worries us is that there is going to be very strong motivation for schools to refuse children with special needs because of the reflection in the tables."
He added that the headteachers involved had been involved in ongoing correspondence with Gwyneth Dunwoody MP and the Department for Education.
Three schools in Nantwich scored 100 per cent for science, Willaston C of E, Weaver and Sound, with Willaston the only school to hit 100 in English.
Weaver Primary hit 92 per cent in English and maths plus 100 per cent in science while Willaston C of E scored 100 per cent in English and science and 94 per cent in maths.
St Anne's Primary scored 95 per cent in English and 90 per cent in both science and maths.
At Wrenbury marks were 85 for English and 92 for maths and science while Wybunbury Delves scored 69 per cent for English, 63 for maths and 88 for science.
Highfield Primary School scored 76 for English, 79 for maths and 83 for science with Millfields gaining 63 for English, 58 for maths and 68 for science.
Cheshire director of education, David Cracknell, warned that parents should not just look at the results and said: "It is necessary to look at more than just performance in these three basic subject areas.
"It is far more important for parents to visit a school, see children at work, talk to the members of staff, and make a balanced judgement about how suitable the school is for child."
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