The Reagan administration yesterday filed its first school desegregation suit, charging that a system of racial discrimination has been maintained at Alabama's public colleges and universities.

In a civil suit filed in U.S. District Court in Birmingham, the government charged that Alabama has "maintained and perpetuated" a "dual system of public higher education based on race."

The suit charges that qualified black applicants have been denied admission to traditionally white schools because of their race; that blacks have been largely excluded from faculty, staff and governing boards of these schools, and that black students have been given fewer opportunities than white students in public higher education.

Assistant Attorney General William Bradford Reynolds, head of the department's Civil Rights Division, said that the suit was filed after more than a year of negotiation with the state failed to produce a settlement. He said that the Justice Department, by filing the suit, does "not intend to discourage further negotiations" and will attempt to resolve the issue "short of full-blown litigation."

The suit comes as the White House is launching a campaign to demonstrate the president's commitment to civil rights in the wake of criticism from minority groups and Democrats that he has turned his back on enforcement of civil rights laws. That criticism intensified after Reagan's recent decision to replace three members of the U.S. Commission on Civil Rights.

Also, there has been a surge in black voter registration and turnout that many Democrats attribute in part to hostility toward administration policies on civil rights and the poor.

Yesterday's suit is only part of the administration's civil rights effort. Attorney General William French Smith has authorized the filing of two more school desegregation suits yet to be announced, Justice Department officials said.

Today, the White House is to unveil the details of Reagan's proposals to put "real teeth" in the fair housing laws. And last month, Reynolds ordered federal examiners into Mississippi counties to register voters.

In the Alabama case, the suit charges that the Alabama officials, including Gov. George C. Wallace and top education officials, violated Title VI of the Civil Rights Act of 1964, which prohibits discrimination by those who receive federal financial aid. The suit also claims the alleged discrimination violates the 14th Amendment to the Constitution, which guarantees equal protection under the law.

The filing of such a suit against Alabama is unusual. By contrast, in settling a long-standing desegregation suit against North Carolina state colleges, the Reagan administration bypassed the attorneys handling the case and accepted a proposal labeled "significantly worse" than plans repeatedly rejected by the Carter administration.

The complaint against Alabama alleges that officials have failed to eliminate "the vestiges" of the "dual system" that discriminated on the basis of race and that they "perpetuated" such a system.

According to the claim, in the fall of 1980, the 16 campuses in question enrolled 77,629 students, including 13,756 blacks, and had 5,132 full-time faculty members, including 394 blacks. The Justice Department said that 14 institutions had white undergraduate enrollments ranging from 56.3 to 96.9 percent, while the two other schools had black enrollments of 76.3 and 99.5 percent.

The suit charges that a racially separate system of higher education was created around Huntsville by the establishment of a branch of the University of Alabama in the area served by Alabama A&M University, a black school. "By creating a racially-dual system of public higher education in the Huntsville area," the state "impeded the desegregation of Alabama A&M," the suit charges.

It also claims that the state has historically provided far greater resources to Auburn University than to Alabama A&M for programs in agricultural education and research. This imbalance was created because of the race of students at each school and has "deprived" students at A&M of equal educational opportunity, the suit charges.