The Justice Department yesterday filed suit against a Chicago apartment complex, charging that a quota system designed to integrate the federally subsidized development illegally discriminated against blacks.

The lawsuit against the nonprofit group of churches and others that own and operate the 309-unit Atrium Village complex alleges that the quota, designed to keep the complex no more than 50 percent black, violated the Fair Housing Act, which prohibits discrimination in housing on the basis of race.

The suit is similar to a New York case in which the Justice Department recently won a court ruling overturning a racial quota at the Starrett City complex in Brooklyn. That ruling is being appealed.

In the Atrium Village case, the Justice Department said, blacks accounted for about 88 percent of the applicants on the waiting list for subsidized units. In some cases, the department said, blacks have waited more than three years for housing while whites who applied later have been offered housing within months.

"Once again, in the name of integration, blacks are being discriminatorily denied housing on the basis of race -- the very evil that gave rise to enactment of the Fair Housing Act in the first place," said Assistant Attorney General William Bradford Reynolds.

Although "integrated housing is certainly desirable," said Reynolds, who heads the Justice Department's civil rights division, "it offends every principle embodied in the civil rights movement to place an artificial, racially-inspired ceiling on the number of housing units to be rented to blacks and other minorities for the benefit of whites."

Michael Shakman, the lawyer for a nonprofit corporation of churches that built the complex, said the U.S. Department of Housing and Urban Development and the Illinois Housing and Development Authority set the quotas to ensure that the complex would be integrated when it was being designed in 1975.

"Our clients are caught in the crossfire between the policies of the Ford administration and the federal courts that approved this project and required the use of quotas, and the zeal of President Reagan's Justice Department to fight affirmative action and quotas wherever possible," Shakman said. "It's terribly unfair to a group of neighborhood churches . . . now getting sued for doing what they were told to do."

He said quotas were necessary in the complex to remedy past discrimination by city and federal authorities that "created an all-black, all-poor public housing system in Chicago . . . . Just as you have to use quotas to desegregate public schools, in this case you had to use quotas to undo the results of unlawful segregation in Chicago," he said.