Academies are using their independence to tailor their intake, establish their own appeals systems for exclusions and to spread the Christian message.
This is the finding of an in-depth TES analysis of contracts signed with academies by ministers.
The funding agreements, released under the Freedom of Information Act, show that at least two academies do not offer children an independent appeal after being permanently excluded.
Agreements also reveal that almost half of the 27 academies - independent state schools, part sponsored and controlled by private finance - select some pupils by aptitude. This compares with only 6 per cent of specialist schools.
This week the Government watered down its education bill after backbench opposition. But plans to set up trust schools, also independent state schools, will remain. Ruth Kelly, the Education Secretary, said trust schools will get a tougher admissions code to stop selection by academic ability.
Andrew Dismore, Labour chairman of the parliamentary joint committee on human rights, said that he was extremely worried about the likely unwelcome consequences for parents' and children's rights posed by trust schools. He cited excluded children's right to an independent appeal and pupils' rights not to be indoctrinated in schools set up by faith groups.
The detailed analysis of academy contracts shows the influence that Christian organisations have over religious education and worship in academies. Funding agreements for King's, in Middlesbrough, and Trinity, in Doncaster, academies sponsored by the Emmanuel Schools Foundation, which are officially non-denominational schools, say they "will have a Christian foundation and will present matters in a way consistent with Biblical teaching".
David Wolfe, education lawyer at Matrix Chambers, London, said academies faced mounting legal threats by parents who say they abuse their independent status.
Academy heads defended the schools, saying that a large proportion had introduced banding tests and admissions lotteries to ensure places were not monopolised by middle-class families. They added that academies, given the power to deviate from the national curriculum, spearhead innovation in the classroom.
A DfES spokesman said: "Academies are required to comply with admissions law. They cannot give preference to pupils on the basis of their parent's occupation or the length of time they have lived in an area."
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