Pupils with SEN account for two-thirds of total exclusions and are four times more likely to be ejected from school than their peers. They are also more likely to come from black, gypsy or Irish Traveller communities, statistics released by the Department for Education and Skills show.
Teachers' leaders warned that ministers' "muddle-headed" approach to SEN has led to thousands of exclusions because of a lack of specialist provision. The resources and teacher training needed to help SEN pupils succeed in mainstream schools have not been provided, they said.
More than 20 per cent of black children and more than a third of gypsyroma and Travellers of Irish heritage are classified as having special needs.
This compares to 15 per cent of white children.
Fears that pupils with SEN and those from ethnic minorities bore the brunt of school exclusions led to the Government introducing targets to cut their use.
Despite success in reducing exclusions by almost a third, the Government was forced to water down its anti-exclusion stance after heads and unions complained that the targets were undermining discipline in schools.
There were 9,535 permanent exclusions during 2001-2, the year after the Government relaxed its guidance. Of these, 1,140 involved pupils with statements and 4,696 identified as having special needs but without a statement.
It is the first time that pupils with SEN but without statements have been included in the figures.
Campaigners have long complained that children with SEN are more likely to be excluded than their peers. The Independent Panel for Special Education Advice estimates that up to 20,000 children with SEN are unofficially excluded from school each year and so do not show up in the Government's figures.
John Bangs, National Union of Teachers head of education, accused the Government of "running down" special schools.
"There are pupils who just cannot cope with mainstream schools without proper one-to-one attention," he said.
A new law intended to give disabled children the right to attend mainstream schools has been labelled a damp squib by campaigners.
The Disability Equality in Education group has accused the Government of failing to publicise the Special Educational Needs and Disability Act after new figures showed that only 181 cases have been lodged with the SEN and disability tribunal.