The top 500 secondary schools take in half as many disadvantaged pupils with special educational needs and disabilities (Send) as the average comprehensive, in what is believed may be a deliberate strategy to boost grades and improve finances.
New research from the Sutton Trust has found that pupils with Send, and especially those who also come from a low-income background, are significantly less likely to attend top state schools, even if there is one in their local area.
The top schools for attainment take in half as many disadvantaged pupils with Send as the average comprehensive, and 36% fewer than live in their catchment area, polling shows.
Nick Harrison, chief executive of the Sutton Trust, said: "It's appalling that many of the top-performing schools take in a lower proportion of Send pupils than live in their catchment area.
"This amounts to further social segregation of the school system, and risks entrenching the double disadvantage faced by low-income families whose children also have Send needs.
"In many cases, schools appear to be actively discouraging applications from Send pupils.
"But we should recognise the tangled web of assessments and incentives, and long-term underfunding, that prevent school leaders taking bolder action on inclusivity.
"This must change if the government is to deliver on its ambition to create more inclusive schools."
The Sutton Trust's polling of more than 2,200 primary and secondary school leaders suggests that many believe schools are deploying a deliberate strategy to control their intakes, with 41% of those leaders thinking that some schools actively discourage applications from pupils with Send - rising to 50% of leaders in schools with the highest proportion of Send pupils.
School leaders thought differing reputations for Send provision (63%) and inclusivity (55%) also played a major role in recruitment, while a third (32%) thought parent's perceptions of a school's approach to behaviour explained different intakes of pupils.
For example, a school that is perceived as being particularly strict may be seen as an unsuitable destination, compared with one seen as being more accommodating to those with additional needs.
The new report builds on previous Sutton Trust research showing the 500 highest performing comprehensives had fewer children eligible for free school meals (FSM) than the national average, and often fewer than their local averages.
The polling also revealed that two-thirds (66%) of school leaders felt that more teachers or teaching assistants were needed to support Send pupils, while 58% wanted more specialist support, such as speech and language support, and 28% wanted better training.
One in four leaders in schools with high levels of Send urged greater recognition of inclusion in inspections and league tables.
The Sutton Trust is calling for the government to reward and celebrate schools that do well with challenging intakes, instead of punishing them in Ofsted and league tables, as well as ensuring that its Send reforms are underpinned by an increased level of funding, teacher recruitment, specialist support and training for mainstream schools.
Margaret Mulholland, Send and inclusion specialist at the Association of School and College Leaders, said: "This research highlights the uneven nature of current Send provision, where schools with a reputation for strong Send support can quickly attract a disproportionate number of pupils.
"The calls for more staff and specialist support to help all schools better educate pupils with Send is revealing and suggests that many schools feel under resourced and in some cases unable to best support pupils with more complex needs.
"Ensuring all schools are able to access the requisite funding, other resources and expertise is crucial to ensuring the success of the government's Send reforms and ensuring all mainstream schools are set up to provide the best possible support to all their pupils."
A Department for Education spokesperson said: "Every child deserves a brilliant education, and schools should serve their communities, not select from them.
"It is completely unacceptable that disadvantaged children or those with Send are being shut out or discouraged from applying - and this government will put a stop to it.
"We are backing this with £3.7bn to create more specialist places, inclusion bases in every secondary school, and stronger accountability - clamping down on off-rolling, tightening oversight of pupil movement, and working with Ofsted to ensure schools are held to account."