The Supreme Court decide 6 to 3 yesterday to nullify rulings that the school systems of Milwaukee and Omaha intentionally maintained racial segregation and sent the cases back to lower courts for consideration.

The Milwaukee school system - one of the nation's 15 largest - has a "neighborhood school" policy dating back to 1919, long before blacks moved to the city in significant numbers. They concentrated overwhelmingly in the north central and northwest sections.

In a decision in litigation begun by blacks in 1965, U.S. District Court Judge John W. Reynolds ruled 11 years later that school officials had engaged in practices intended to create and maintain a segregated school system. The officials insisted the practices merely preserved the pre-existing policy of assigning students to schools near their homes.

Reynolds prohibited future discrimination and ordered desegregations plans drawn. Last July, the Seventh U.S. Circuit Court of Appeals let his ruling stand, concluding that he "was not clearly erroneous" in finding that the officials had sought to isolate blacks.

In an unsigned opinion, the Supreme Court faulted the lower courts for not heeding the guidelines indicated in earlier cases and explicitly ordered followed in a Monday decision involving the Dayton schools: determining the "incremental segregative effect" of constitutional violations on the distribution of students, comparing that distribution with what it would have been without violations, redressing that difference, and providing a system-wide remedy only if there has been a system-wide impact.

Justice John Paul Stevens, in a dissenting opinion joined by Justices William J. Brennan Jr. and Thurgood marshall, protested that the appellate court neither had before it nor had considered a desegregation plan. As a result, he said, "there is nothing for it to reconsider . . ."

He accused the majority, acting on the final day of the term, of "hasty action" that "will unfortunately lead to unnecessary work by already overburdened circuit judges who have given this case far more study than this court had time to give it."

The Omaha case involved 99 schools in the city and part of Sarpy County. Half of them had 80 per cent to 100 per cent black enrollments. Of 39 new schools opened between 1951 and 1973, 37 were either predominantly black or predominantly white. As in Milwaukee , school officials said they adhered to a neighborhood school policy.

Two years ago, the Eighth U.S. Circuit Court of Appeals concluded that the evidence establised that the Omaha school district "intentionally created and maintained" segregation, the district having failed to prove it wasn't motivated in part by bias. The court approved a desegregation plan that would have relied on systemwide busing, among other techniques.

The government, which had sued the district in 1973, said the plan went too far. Yesterday, citing the Dayton guidelines, the Supreme Court, in another unsigned opinion, agreed.

Dissenting, Brennan, joined by Marshall and Stevens, wrote that the comprehensive desegregation plan was "entirely appropriate," because anything less would simply not correct Omaha's "massive systemwide intentional segregation."

In another case, the court denied a General Motors Corp. petition for a review of a ruling that it had discriminated against blacks in promoting employees at its Chicago Distribution Center, the largest nonunion GM facility in the country.

The case lost by GM involved the job of hourly clerk, historically a stepping stone to coveted salaried posts. In 1973, when the work force was 25 per cent black, the hourly clerks were 100 per cent white; in 1975, 28 of 31 hourly clerks were whites - with all three blacks working nights.

A U.S. District Court judge, upheld by the Seventh U.S. Circuit, ruled that GM had to, but didn't, prove that it did not discriminate against blacks as a class. GM, claiming it merely had followed "a bona fide seniority system," objected that the ruling was based "salely on statistics."