The University of North Carolina, charging that Secretary of Health, Education and Welfare Joseph A. Califano Jr. is seeking to tamper with its academic freedom, filed suit yesterday to prevent Califano from cutting off $90 million in U.S. aid funds.

With former civil rights lawyer Charles Morgan acting as its attorney, the university chose a court in its own backyard, the federal court for the Eastern Distric of North Carolina in Raleigh, to petition for an injunction against a fund cutoff. Previous action in the long-running dispute over ending vestiges of segregation in the 16-unit university system has been in federal district court in Washington, D.C.

The University's suit, raising numerous legal objections to the threatened fund cutoff, is the latest legal twist in a dispute going back nine years and involving six southern states. All the other states have adopted HEW approved plans to end the vestiges of segregation but no compromise was reached with North Carolina.

Califano announced March 26 that he would start proceedings to cut off federal aid funds to the university unless a compromise was reached.

Negotiations since then produced an offer by North Carolina to put $41 million into beefing up its five traditionally black colleges and improving their facilities and programs-but no agreement on the crucial question of ending duplicate advanced and specialized programs at traditionally black and tradionally white schools located near each other. HEW and others have argued that white students are unlikely to seek admission to the five virtually all-black schools unless these are the only places they can enroll in the programs they want to specialize in.

Califano told reporters Monday that the university had refused to make two commitments on duplication he considered essential: that if the enhancement programs at the five traditionally black colleges don't bring in more white students by the end of two or three years, then all duplication will be ended; and that the state pledge not to install new programs in the traditionally white units that would have the effect of impeding development of the black schools.

Yesterday the university, in its petition, said the HEW attempt to tell the university in shift programs from one school to another interferes with academic freedom and states' rights under the Constitution. It also argued that various regulations under which Califano is acting were improperly drafted or issued, and that Califano is improperly using numerical goals and timetables of black-white ratio as indices of vestiges of segregation.