The Oxford University study found that black Caribbean pupils, including those with mixed heritage, are twice as likely to be identified as having a social, emotional or mental health need as their white British peers.
Black Caribbean and Pakistani pupils are also over-represented in terms of the identification of moderate learning difficulties.
Racism from teachers, a lack of understanding of cultural differences and ineffective classroom management are among possible factors cited in the report behind the over-representation.
Another factor could be black pupils being more at risk of developing social, emotional or mental health problems and moderate learning difficulties due to poverty.
The research points out that while 14 per cent of white British pupils are eligible for free school meals, the figure rises to 25 per cent for black African pupils, 28 per cent for black Caribbean pupils and 29 per cent for mixed race Caribbean pupils.
"A frequently proposed explanation for the over-representation of black pupils with social, emotional or mental health problems and moderate learning difficulties is inappropriate interpretation of ethnic and cultural differences including teacher racism, low expectations and a failure of schools to provide quality instruction or effective classroom management," states the report.
"However, an alternative hypothesis is that disproportionality reflects the fact that ethnic minority pupils are more at risk [of these problems] because of the substantially greater socioeconomic disadvantage they experience relative to the white majority."
Researchers highlighted that children wrongly identified with a special educational need could see their education suffer as a result.
Report author Steve Strand, professor of education at Oxford University, added: "Some black Caribbean children may be suffering an inappropriate or narrowed curriculum from unwarranted over-identification, particularly in secondary school."
The report also found that Asian pupils are "substantially under-represented" in the identification of social, emotional or mental health problems and autistic spectrum disorders.
Strand said that this could mean that many Asian pupils with these conditions are not being diagnosed and are missing out on support, for autism in particular.
"The upshot is that some Asian pupils may not be receiving the access to specialist resources and support they need with autistic spectrum disorders," he said.
The report suggests that lower awareness of autism among Asian communities could be a factor, as could the possibility that diagnosis would be stigmatising.
"In any event, there is a need to raise awareness of autistic spectrum disorders among Asian communities, improve outreach and review the extent to which services are configured appropriately," the research states.
The research has also produced individual reports for 150 councils on their ethnicity and special educational needs data.
This found that while location was not a major factor in over- and under-representation among ethnic groups there were some notable local differences.
An example is that in the London borough of Newham, black Caribbean pupils were less likely than their white peers to be identified with social, emotional or mental health problems, but were three times more likely in the London Borough of Kensington & Chelsea.