The study blames a retreat from desegregation since the civil rights movement, along with patterns of housing discrimination and increased immigration in many urban areas.
Seventy per cent of America's black students and over 33 per cent of Hispanic students attend predominantly minority schools, while most white students attend schools with mostly other whites.
"Though our schools will be our first major institutions to experience non-white majorities, our research consistently shows that schools are becoming increasingly segregated and are offering students vastly unequal educational opportunities," says Gary Orfield, a professor at the Harvard Graduate School of Education and co-director of the Harvard Civil Rights Project, which conducted the study.
The findings come after other research has found that desegregated schools boast higher standardised test scores and higher student self-image. Minority students who attend integrated schools have been found to be much more successful at university.
The number of blacks and Hispanics in America is increasing at about the same rate that the number of whites is declining.
The proportion of blacks in predominantly non-white schools has more than doubled since 1980, when it was 33 per cent. There has also been marked resegregation in the South, which after the era of desegregation had become the nation's most integrated region.
More than one-third of Hispanic students attend schools in which 90 per cent or more of students are non-white, up from one-quarter of Hispanic students in 1968.
But the most segregated group is whites, who on average attend schools where fewer than 20 per cent of the enrolment is comprised of racial minorities.
Segregation remains closely tied to income. Predominantly non-white schools almost always also have high concentrations of poverty.
The Harvard researchers recommended that high-quality schools be opened to attract whites to predominantly non-white inner cities, and that community groups should attempt to force school desegregation through the courts, much as they did in the 1960s.