CONGRESS HAD PACKED its bags until Labor Day and the sultry air had chased most of Washington's residents out of town when the Reagan administration launched a legal assault on the civil rights law mandating equal treatment for women in federally funded schools.

The law is one many women's groups see as their modern-day bill of rights. The battleground is the Supreme Court. The potential victims are legion: not only women -- whom President Reagan recently has tried to placate -- but blacks, Hispanics, disabled individuals, and past and present victims of discrimination who have looked to the federal government as their prime protector.

There is one other potential victim: the administration's much-vaunted "Baby Doe" rule requiring treatment for handicapped newborns in medical facilities receiving federal aid.

One of the most telling ironies of the Justice Department attempt to limit Title IX of the Education Amendments of 1972 is that the Baby Doe rule is based on a civil rights statute nearly identical to Title IX. Title IX says if colleges and universities get federal student aid, they can't discriminate against women. "Baby Doe" says that if hospitals get Medicare and Medicaid, they can't discriminate against handicapped babies.

It is difficult to see how the administration will be able to argue that Title IX's antidiscrimination provisions reach no further than the direct "program or activity" receiving federal aid -- the financial aid office of a college, as opposed to its athletic program -- and still argue that a similar civil rights rule can reach into a hospital nursery.

Nurseries, after all, don't cash federal Medicaid checks. If Medicaid and Medicare were considered "program-specific," benefitting only the part of the hospital they touch directly, the Baby Doe rule would be left hanging by a legal thread.

The fact that it would have any legal basis at all in the brave new world of "program specificity" is because Assistant Attorney General for Civil Rights William Bradford Reynolds saw the conflict coming months ahead of time. He lobbied successfully for inclusion of a separate -- albeit tenuous -- legal underpinning for the Baby Doe rule.

It should be said that, as obnoxious as most women's groups and the U.S. Commission on Civil Rights have found the solicitor general's brief in Grove City College v. Bell, it is not as bad as it could have been. The school, which has never been charged with discrimination, has failed to sign a statement of compliance with Title IX, arguing that Pell Grants, student loans and the like are not "federal financial assistance" to the school, but to the students.

The administration could have adopted that logic and capitulated. It didn't. But its call for "program-specificity," the legal shorthand for limiting the reach of Title IX, still represents a radical break with more than 10 years of legal reasoning by both Democratic and Republican administrations.

It would give a school license to discriminate in course offerings, athletic programs, housing, hiring, admissions -- any program not receiving direct federal aid. Student aid would oblige the college to refrain from discrimination only in its financial aid office.

Justice's timing is, to say the least, unfortunate. Perhaps the leaders of Justice's Civil Rights Divison should be pitied for having to play the heavy just when the administration's public-relations machine has been spinning out images of the president's sensitivity for the poor, blacks, women and the disadvantaged.

But Justice did then come along and, in three short but devastating pages of a 50-plus page brief, threaten to eviscerate a key element of federal civil rights enforcement. The three major antidiscrimination laws -- Title VI of the Civil Rights Act of 1964, Title IX and Section 504 of the Rehabilitation Act of 1973 -- all have virtually identical clauses prohibiting discrimination in any "program or activity" receiving federal aid. By narrowing the definition of "program or activity," Justice would be turning the goverment's two-decade marathon antidiscrimination effort into a one-legged race.

Why bother? Because, Attorney General William French Smith wrote in a letter to an incredulous Sen. Robert Dole (R-Kan.), Justice's view of the case represents "the most reasonable reading of the statute and its history. I am disappointed you find this so 'difficult to understand.' "

But 225 members of Congress and several previous Justice Departments and the U.S. Commission on Civil Rights read the law differently. In the closing flurry of legislation last week, resolutions were introduced in both the House and Senate urging a broad interpretation of Title IX, providing that the receipt of any federal aid, no matter for what purpose, obliges an institution to refrain from discriminating in all its programs.

In a statement released last week, the Civil Rights Commission argued "this position would open the door to renewed federal financial support for discriminatory activity across the spectrum of American life."

The Supreme Court has thus far avoided a direct ruling on the issue of program specificity. Whatever ruling is finally made, in this case or others, will have serious implications for every major civil rights law that depends on the threat of a federal-fund cutoff to encourage compliance by schools, contractors, hospitals, housing project developers and the like.

Political acceptance of Title IX is widespread: the law and the climate that created it are credited with the dramatic increase of women in graduate and professional programs. Since 1971, commission member Jill Ruckelshaus has pointed out, the number of doctoral degrees awarded to women has doubled and the percentage of women law school graduates more than quadrupled.

Which brings us back to the Baby Doe rule, an icon of the right-to-life groups. Speaking to a group of evangelical ministers, President Reagan committed himself, in the strongest terms, to protecting the rights of handicapped newborns. The message: they have civil rights too; retarded infants cannot be starved to death.

But if Medicare and Medicaid, the main forms of federal assistance to hospital, are considered "program- specific," handicapped babies would be protected by direct federal intervention only if they happened to be born in the business office.