The Government has admitted that academies do not have to admit children with special needs.
In a letter to England's 150 local councils, the Department for Education and Skills said children with emotional, behavioural and physical difficulties "do not have a statutory right" to choose an academy on school admission forms.
Ian Coates, head of the DfES special needs and disability division, said councils should not force academies to take children with special needs, even though they can force other state schools to do so. He said exercising the same control over academies would undermine their status as independent state schools.
Martin Rogers, co-ordinator of The Education Network, a local authority research unit, estimated that clashes with academies over special needs admissions would rise as the Government attempts to open 200 of the schools by 2010. At present, there are 27.
He said proposals in the white paper, which recommends that all new secondary schools be run by charitable trusts, independent of local council control, would further marginalise special needs children.
"Academies are meant to be the Government's flagship schools for the disadvantaged and the model for many aspects of the new trust schools," he said.
"The white paper promotes a new role for local authorities as a commissioner of services instead of a provider. Their ability to do this effectively is obviously undermined by such different treatment for academies."
Mr Coates said normal state schools must admit a child if a council disagrees with its decision to refuse a place, though the same rule does not apply for academies, which also need not follow the national curriculum and can alter teachers' contracts. He said: "Where the academy is of the opinion that the child's attendance at the school would be incompatible with the efficient education of other children, the local authority should not name the academy."
The DfES has already set up a dispute resolution service to intervene when councils and academies are at odds over the admissions or statements of special needs pupils. The service tries to resolve disputes before they go to the SEN and disability tribunal. The tribunal has considered 11 appeals involving academies: seven were upheld, three dismissed and one struck out as it fell outside the tribunal's remit. In 200304 it considered 3,637 appeals nationally.
Last year an analysis of three academies by Professor Stephen Gorard, of York university, suggested the schools were raising standards by improving their intake. Only one, Bexley academy, London, was found to still serve the most disadvantaged children. Figures released to Parliament this summer show most academies have fewer deprived pupils than the schools that they replaced.