A letter from the Department for Education and Skills, sent out to all chief education officers and directors of children's services last month, shows that parents could be denied a place for their child and local authorities have no power to help them.
Under arrangements for admission to maintained schools, parents with a child with special educational needs can express a preference for a school place. Local authorities then consult the school and may name the school as suitable on the pupil's statement.
However, if an academy chooses not to accept a pupil, the local authority cannot name it in the child's statement.
The position has been clarified in a letter from Ian Coates, head of special educational needs and disability division at the DfES. It says:
"Parents do not have a statutory right to express a preference for an academy, though they can make representations as to the particular academy they would like their child to attend.
"Where the academy is of the opinion that the child's attendance at the school would be incompatible with the efficient education of the other children and there are no reasonable steps that could be taken to prevent that incompatibility, and, consequently, does not consent to being named in the child's statement, the local authority should not name the academy."
If the matter is disputed by the authority or parents, it may be referred to the Academies SEN Dispute Resolution Service set up by the DfES. The final decision on whether the school is named may rest with the Secretary of State.
The letter continues: "Once named in this way, the academy must admit the child in accordance with the terms of its Funding Agreement with the Secretary of State."
But Martin Rogers, co-ordinator of The Education Network, said: "This letter spells out rather starkly that parents of some of our most vulnerable and disadvantaged children have no statutory right to choose an academy.
"As the number of academies rises, this problem will grow. In some disadvantaged areas there are already plans for several academies to replace existing maintained schools, so parents of children with special needs will find their right to 'choose' a school increasingly restricted."
Mr Rogers added that the power of local authorities to act as a champion of services for parents and children will be "obviously undermined by such different treatment for academies".
"This illustrates very clearly the fundamental importance of having fair admissions arrangements for all children right across every type of school in the state system," he said.