Many schools are " institutionally racist" and expel black pupils three times as often as other children, according to a Government-funded report.
A "significant minority" of primary and secondary schools in England are failing to observe race-relations laws, the two-year study concluded.
Schools must work more closely with black parents to stop children being expelled without good reason, the research said.
Teachers' leaders and the Commission for Racial Equality described the conclusions as worrying.
But the Government insisted "rapid progress" was being made on tackling higher rates of school exclusions among black pupils.
The report comes amid concerns over continuing poor exam results among black pupils across England.
The latest Government figures, published last month, revealed a continuing gulf between the performance of black teenagers and their white classmates at GCSE.
Academics at Canterbury Christ Church University College examined figures for 800 excluded pupils from 85 primary, secondary, special schools and pupil referral units.
One of report's authors, Professor Carl Parsons, said the problem was not about racist individuals, but school policies that resulted in discrimination.
"Some argue that this is the new racism," he said. "It's not about skinheads on the street shouting nasty names at dark-coloured people.
"Individuals assessing children say, 'We are judging people by their characters and not the colour of their skin'."
The research, conducted for the Department for Education and Skills, found black Caribbean pupils were more than three times as likely to be expelled as white pupils.
The researchers found nearly one in ten secondary schools did not understand their obligations under the Race Relations (Amendment) Act of 2000.
A spokesman for the CRE said: "These findings are a cause for concern."
A DfES spokesman said the report "does not say that all schools are institutionally racist - nor do we believe that they are".