When President Bush flew into John F. Kennedy International Airport June 19, Mayor Bloomberg was out on the tarmac to greet him. The two engaged in some friendly backslapping and reporters wrote stories about the occasion.

The president’s relationship with New York City, however, is not always as amicable. In federal courts in Manhattan and Brooklyn, Mr. Bush’s Justice Department has brought half a dozen cases against the city’s public agencies. With each settlement, the federal government has won a degree of oversight over local government.

Because of the lawsuits, federal attorneys in Manhattan now monitor job promotions at the Department of Parks and Recreation to guard against racial discrimination. In May, the Justice Department required the city to notify welfare-to-work employees that they have the same protections against harassment as full-time municipal workers. Just one day after the president’s June visit, Mr. Bush’s lawyers accused the New York City Transit Authority of harassing a Sikh employee.

Last week, the Justice Department forced the transit authority to cough up $165,000 for failing to repair leaky airconditioning units on old subway cars. That settlement came six years after one with the sanitation department over the city’s disposal of discarded appliances containing Freon.

“The feds are the biggest bureaucracy of all, and when they make rules and try to make other people follow their rules it takes forever to untangle,” the president of New York Civic, Henry Stern, said. “The public is unaware of the substantial invasion of traditional local government prerogatives by federal agencies and their attorneys.”

Mr. Stern, who, as a former parks commissioner, was accused of racial discrimination in a Justice Department suit, called the federal efforts against the city an affront to taxpayers.

“The taxpayer pays for both sides and no matter who wins, we lose,” he said.

A list compiled by The New York Sun shows that the Justice Department has filed five lawsuits against the city or the New York City Transit Authority since Mr. Bush became president in 2001.Also, it filed criminal charges against the city’s Department of Environmental Protection for a mercury spill that was ignored. The city agency pleaded guilty in 2001.

In each lawsuit, the city and the federal government have arrived at a settlement, the terms of which generally allow the federal government to monitor the city’s conduct for a period of three years. When the allegations involve discrimination, the federal government generally requires the city to take corrective actions, such as sending out public notices or putting in place a person responsible for fielding complaints. Large cash penalties rarely accompany the settlements.

This is an arrangement that likely suits both sides, a senior fellow at the Manhattan Institute, Walter Olson, said.

“City agencies would rather have some marching orders— even ones they don’t like — than being entirely uncertain of what the law is going to demand of them in court,” Mr. Olson said. “And prosecutors like the kind of track record that shows they can compel quick capitulations.”

The strategy often prevents a public accounting, because most of the discussions take place out of court. In one case, involving Lafayette High School in Brooklyn, Justice Department attorneys filed a settlement on the same day as the legal complaint, indicating that the lawyers for the two sides had hammered out an agreement before they ever went before a judge.

The only open case the Justice Department still has in courts against a city public agency is a challenge to the transit authority’s dress code. The lawsuit claims that a ban against turbans for employees who interact with passengers is discriminatory against Sikh and Muslim workers. The transit authority’s dress code has been changed: Employees are now permitted to wear transit authority-issued turbans bearing the MTA logo.

The federal government is arguing with the transit authority over an informational flyer that features a photograph of a Sikh transit authority employee wearing a turban with the logo. Since July, the Justice Department has demanded the photograph of the employee, station agent Trilok Arora, be removed from the flyer. Mr. Arora said he disagrees with the dress code. The transit authority is willing to remove the photograph only if the Justice Department pays a model to don the turban and appear in Mr. Arora’s place, according to court papers filed by the government.

When the federal government presses the city in court, it often files a complaint similar to one that private attorneys have already filed. In a dispute over job promotions at the parks department, the Justice Department followed the lead of a class action filed in 2001. Both lawsuits accused the parks department of passing over career employees, many of whom are black or Hispanic, for promotions that went to young and mostly white recruits who just graduated from college.

Under a settlement reached in 2005, the Parks Department must post all job openings and expand personnel files to provide a better basis for promotional decisions. The city also began sending records of recent promotions at the department to the federal government for review, a lawyer familiar with the case said.

An attorney for the class action against the Parks Department, Lewis Steel, said the Justice Department’s decision to file suit adds credibility to the claims made in the private lawsuit, which has not yet been resolved.

The Justice Department has taken the city to court over allegations of assaults and harassment against Asians in a Brooklyn school, Lafayette High School in Bensonhurst. Three years after initiating an investigation, the federal government reached a settlement with educators in 2004 that required the school to keep a detailed record of every complaint of harassment.The settlement also set guidelines meant to bolster the English Language Learner program. The school continues, through next year, to be under the watch of the federal government.

Perhaps the largest degree of control the Justice Department has gained through the courts over any current city undertaking involves the water filtration plant under construction in the Bronx.The $1.2 billion plant, which is to be placed beneath Van Cortlandt Park, will eventually treat all city water from Croton watershed in Westchester County. Throughout the 1990s, the city had sought to avoid building the water treatment center, claiming that the city could protect the water by guarding against pollution at the sources. Although a 1998 court settlement with the Environmental Protection Agency required the city to build the plant, choosing a location required legislation from Albany, which passed in 2003.The city’s law department now files monthly reports to the EPA and holds quarterly meetings to provide updates on its progress, a lawyer familiar with the case said. The city has been hit with more than $6 million in penalties following the settlement.

Despite these lawsuits, some New Yorkers think the Justice Department occasionally shies away from a fight. A vice president with the Vulcan Society, the city’s fraternity of black firefighters, Michael Marshall, said the Justice Department “has never been really receptive” to his organization’s claims that the department’s hiring practices are discriminatory. Conversations between the Justice Department and the Vulcan Society over the small number of black firefighters extend back nearly two decades, Mr. Marshall said. Last year, the Justice Department confirmed that it had begun an inquiry into the fire department.

Legal observers warn against judging the track record of either the city or the Justice Department from the docket of cases the federal government has brought against the city.

“It could mean the Department of Justice is handling everything exactly right and policing what needs to be policed,”a law professor at New York University, Samuel Issacharoff, said. “Or it could mean they are asleep at the switch.”