In a report to be published later this month, the Audit Commission, the public sector's independent financial watchdog, will call for action to tackle a "complex web of factors" which prevent or discourage many mainstream schools from meeting the needs of pupils with SEN.
These include a lack of both resources, and of knowledge and skills of teachers in addition to the pressure of league tables and the way special needs education is managed in schools.
"Some schools show enormous commitment to working with children with SEN; others are not playing their part fully," said Anne Pinney, manager of the Audit Commission's project.
The report will call for teacher training to give greater emphasis to skills such as behaviour management that teachers need if pupils with SEN are to be fully included in mainstream education. It will also say that monitoring and accountability of the effectiveness of education for pupils with special needs must be improved.
It will be the second report that the Audit Commission has published on special needs in the past six months. In June, the commission called for reform of the system which requires statements of need to be given to children with severe special needs.
The Special Educational Needs and Disability Act 2001 gave parents of children with SEN the legal right to have their children educated in a mainstream school unless it would harm the education of other children.
The Audit Commission report will be available from www.audit-commission.gov.uk