The study, by researchers at Harvard's Graduate School of Education, found that the period between 1991 and 1994 saw the largest backward movement toward segregation since the landmark 1954 Supreme Court decision Brown versus Board of Education, which brought an end to the legal separation of racial groups in schools.
"In American race relations, the bridge from the 20th century may be leading back into the 19th," it said.
This new segregation stems from demographic patterns that have stranded minority students in inner-city schools as the non-white population becomes increasingly confined to urban areas and jumps exponential ly in size.
The number of Hispanic children in the United States has grown by 178 per cent in 25 years, and the number of blacks by 14 per cent, while the number of whites has fallen 9 per cent. Nearly one-third of all minorities are enrolled in the 10 biggest metropolitan school systems.
Three-quarters of Hispanic students attend schools where most of the other students are also Hispanic, researchers calculated using federal enrolment statistics. Two-thirds of blacks attend predominantly black schools.
"We're headed toward increasing racial and economic polarisation in our schools, and that's going on particularly in places where we had the most success with the civil rights revolution, namely, in the south," said Gary Orfield, a Harvard education professor and the principal researcher.
Schools that serve predominantly minority enrolments also tend to be in economically impoverished communities, the study found.
"We don't know how to make schools work where there is concentrated poverty," Dr Orfield said. "And if we isolate a growing part of our population in schools that we don't know how to make work, and we make going to college a prerequisite for most employment, then we're inviting a catastrophe."
While segregation previously was eased by transporting students from ethnic neighbourhoods in one part of a city to another, these more recent demographic changes will require a change in housing patterns or busing students from the cities to the suburbs - a politically divisive proposition.
"It can't be solved inside the central cities," Dr Orfield said. "We really need to have an overall strategy to address all of these dimensions."