A settlement between the city’s public schools and the federal government, meant to remedy discrimination against minority and female school custodians, in fact unconstitutionally discriminated against white male employees, a federal judge ruled yesterday.

The case is noteworthy because many of the figures involved in the 1999 settlement that the federal judge struck down are prominent public figures to this day. The assistant attorney general in the Justice Department who oversaw the case, Deval Patrick, is a leading candidate for governor in Massachusetts in a Democratic primary to be held a week from today. The mayor of New York City who agreed to the settlement, Rudolph Giuliani, is a former associate attorney general of America who is a potential 2008 presidential candidate. And the New York City schools chancellor who agreed to the settlement, Rudolph Crew, is now superintendent of Miami-Dade County Public Schools, the nation’s fourth-largest school district.

The case also is somewhat unusual in that it is a setback to racial preferences as a remedy to discrimination issued by a judge, Frederic Block of U.S. District Court in Brooklyn, who was appointed by President Clinton, a Democrat. Democratic-appointed judges have tended to be less willing to strike down racial preferences for minorities or “affirmative action” as unconstitutional, and the issue was a subject of intense questioning during the confirmation hearings of President Bush’s Supreme Court nominees by Democratic senators who appeared to fear that the Bush nominees would do what Judge Block has now done — rule that a remedy designed to cure unlawful discrimination against blacks or women is itself unlawful discrimination against whites or men.

The federal judge yesterday described as unconstitutional a key component of the settlement. The troubling component granted retroactive seniority to dozens of minority and female custodians who were permanently hired as part of the settlement. Judge Block ruled that in the event of layoffs, the retroactive seniority granted to the new hires meant that white male employees would be the first to lose their jobs.

Judge Block said courts have rejected “race-conscious layoffs” as a violation of the 14th Amendment guarantee of equal protection when the employer is a public agency, as it is in this case.

In so ruling, Judge Block sided with several white custodians who had objected to the settlement.

The hiring of school custodians, who are the equivalent of building superintendents and have staffs beneath them, has been a disputed matter for more than a decade. The Justice Department first presented its case publicly in 1994, when, according to a news report from the time, federal attorneys sent letters to the city alleging that the written examination used to hire custodians had not been shown to be job-related and resulted in the hiring of few minority candidates. A letter that Mr. Patrick, then with the Justice Department, sent to city officials noted that of the 865 school custodians employed in 1993, 4.2% were black, 3.2% were Hispanic, and 0.5% were Asian, according to news reports.

A settlement reached in 1999 extended permanent employment to 59 black, Hispanic, Asian, and women custodians and granted them certain benefits, such as backdated seniority. Many of them were already working as custodians, but had been hired as provisional status and were not accruing seniority. Only seven candidates were able to show that they had been actual victims of discrimination, Judge Block said.

Since then several white custodians, who say their seniority was disadvantaged by the agreement, have fought the settlement. The case has bounced around the courts as the four white custodians successfully appealed a magistrate judge’s decision that rejected their petition to intervene in the case.

In his ruling yesterday, Judge Block rejects several points raised by the four men — John Brennan, James Ahearn, Dennis Mortenson, and Scott Spring. But he ruled with them on another question. Their attorney, Michael Rosman of the Center for Individual Rights in Washington D.C., had argued that the retroactive seniority gave minorities and women a competitive advantage in vying against white male custodians for higher-paying custodial jobs.

“They settled this on the backs of their current employees,” Mr. Rosman said. “If there were a real problem, the defendants could have paid out money to people who were allegedly discriminated” against.

The Center for Individual Rights is the organization that brought landmark lawsuits against the University of Michigan and its law school that the Supreme Court ruled on in 2003.

Legal observers have said it was unusual to grant alleged victims of discrimination retroactive seniority, as the city and the Justice Department agreed to do in this case.

Judge Block ruled that many aspects of the settlement were legal, including the comparative advantage that the seniority granted new hires when they applied for transfers and higher-paying jobs.

But he found that the advantage the seniority gave to the minority hires was unconstitutional because of the possible advantage it would provide during layoffs. To receive such protection, Judge Block ruled that the hires had to do more than simply be hired under the settlement agreement. They needed to be able to prove they were actual victims of racial discrimination.

In his 91-page decision, Judge Block described the case as a “legal juggernaut,” and wrote that of the related court cases he is aware of “none has approached the complexities of this case.”

Still there was one issue that he was able to settle without a constitutional analysis. Judge Block found that one man who had received benefits under the settlement and is identified as Hispanic in Board of Education records, Ciro Dellaporte, was in fact of Italian ancestry and lacked all “cultural or linguistic ties to a Spanish-speaking country.”

In his ruling yesterday, Judge Block encourages the two sides to reach an out of court settlement based on his ruling.

When contacted yesterday, spokesmen for the Justice Department and the city’s law department said they could not comment because they had not yet seen the decision.

A campaign spokeswoman for Mr. Patrick declined to comment yesterday evening.

Mr. Patrick and Mr. Crew are black; Mr. Giuliani and Judge Block are white.