The investigations, known as “secretary-initiated cases” to indicate their importance, had been used in the past to set precedent and to put other localities and developers on notice.
One of the delayed investigations looked at an ordinance in Hesperia, Calif., that prevented the siting of neighborhood group homes for parolees and former offenders throughout the city’s neighborhoods. HUD investigators saw the case as an important test of the federal resolve to rehabilitate low-level offenders, who often face housing and job discrimination when they are released, leaving them in need of government assistance.
Other cases that were held up involved questions about the accessibility to the disabled of new dwellings built by a pair of large residential construction companies, Toll Brothers and Epcon Communities, in New York City and Ohio, according to a department official.
One high-profile case never made it to that stage.
HUD had opened a case in late 2016 in response to a ProPublica article that said Facebook gives advertisers the ability to exclude specific groups it calls “ethnic affinities” from seeing their ads when their social media habits identified them as black, Hispanic or Asian-American.
But even before Ms. Farías was appointed, Mr. Carson’s aides ordered fair housing division officials to cancel a planned negotiating session with Facebook executives, leaving HUD to take Facebook at its word that the company’s “policies prohibit using our targeting options to discriminate.”
Then, after taking office, Ms. Farías sent a one-page letter to Facebook ordering, without explanation, the termination of a preliminary investigation into the company’s advertising practices.
Fair housing groups filed a lawsuit on Tuesday in Federal District Court in Manhattan saying that Facebook continues to discriminate against certain groups — including women, veterans with disabilities and single mothers — in the way that it allows advertisers to target audiences for their ads.
Ms. Farías, an official at HUD in the George W. Bush administration, has not initiated any high-priority cases of her own, according to agency officials. And she has made it clear that she does not intend to aggressively pursue cases that are not instituted “by my secretary,” meaning Mr. Carson, according to an official who spoke with her last year.
“For all intents and purposes, this administration is stopping the enforcement of civil rights and fair housing laws at the worst possible time,” said Gustavo Velasquez, who served as assistant secretary for fair housing during the last three years of President Barack Obama’s administration.
“It’s not just the lack of an agenda, which is what I thought we were dealing with for the first year or so, but an attempt to reverse all the advances we made through regulations and enforcement actions,” said Mr. Velasquez, who now works for the Urban Institute, a nonpartisan progressive think tank in Washington.
This is not the first time critics have accused Mr. Carson, the only African-American man in President Trump’s cabinet, of trying to stymie civil rights enforcement. Shortly after he was confirmed last year, Mr. Carson tried to reverse an Obama-era program that would make it easier for recipients of housing vouchers to use them in affluent neighborhoods.
The move was struck down by the courts, and Mr. Carson abandoned the effort.
Last week, Mr. Carson told members of the Senate Banking Committee that he planned to delay another Obama-era rule that would have required local governments to create detailed plans to integrate racially divided neighborhoods. And a provision barring localities from using federal funding to undertake such programs was stealthily inserted into the 2018 spending plan passed last week by Congress.
Despite these moves, Mr. Brown, the HUD spokesman, said the department was merely “looking to streamline” its enforcement efforts and to focus on new, neglected areas of discrimination.
“There is no mission shift. We are, in fact, putting more emphasis in sexual harassment” complaints, Mr. Brown wrote in an email. “In addition, 60 percent of the fair housing complaints we receive are disability related, and the majority of those have to do with service animals.”
The most significant fight over fair housing under Mr. Trump is taking place in Houston, a sprawling metropolis ranked in numerous studies as one of the United States’ most segregated cities, where overt opposition to a housing development based on race and income has drawn the attention of career HUD investigators.
In January 2017, before Mr. Obama left office, HUD lawyers accused Houston officials of violating fair housing requirements cited in the 1964 Civil Rights Act. The city’s mayor, Sylvester Turner, a Democrat, had killed a 233-unit mixed-income, mixed-race housing development slated for an affluent white area known for its high-end shopping and excellent schools.
HUD told the city to undertake specific remedies as a condition of continued funding, including the approval of the development, known as the Fountain View Project, and the adoption of tough new zoning laws.
In a scathing letter, HUD officials accused Mr. Turner, who is African-American, of succumbing to “racially motivated local opposition,” claiming that he caved to protests by white business owners and residents.
Mr. Turner has denied the accusation, arguing that he opposed the development because only 23 apartments were set aside for low-income families. He also objected to the idea of forced integration, putting him in agreement with Mr. Carson.
“I have chosen to stay in the neighborhood where I grew up, and I will not tell children in similar communities they must live somewhere else,” said Mr. Turner, who grew up in an all-black development.
But he might have had other reasons for opposing the project. In one meeting, Mr. Turner privately admitted that he hoped his position on the project would coax white Republican state legislators to support a bill needed to restructure Houston’s ailing pension system, according to a former federal official who attended the meeting.
The mayor denied that account.
“He never told anyone he opposed the Fountain View Project to win votes for his pension overhaul,” said Mary Benton, a spokeswoman for Mr. Turner.
Still, few Democrats have done quite so well in negotiating with the Trump administration as Mr. Turner, who began pressing Mr. Carson to release the city from the order shortly after Mr. Carson was confirmed.
Ms. Farías, with Mr. Carson’s blessing, began negotiating directly with Mr. Turner and other city officials. She largely excluded the career lawyers who had already begun drafting a tougher order — one that required the city to pay the Houston Housing Authority, Fountain View’s developer, as much as $14 million if it insisted on blocking the deal, according to an official in Houston.
But Mr. Turner, who believes the case to be a distraction from his city’s rebuilding effort, prevailed.
This month, Ms. Farías signed a new, less stringent agreement that other Houston officials eager to get federal money flowing into hard-hit neighborhoods — including Representative Al Green, a Democrat and harsh Carson critic — hailed as a victory. But a coalition of local advocacy groups and national organizations are suing to block the disbursement of $5 billion in HUD recovery money unless the city abides by civil rights-era fair housing laws.
“If this isn’t a violation of Title VI of the 1964 Civil Rights Act, then damn it, I don’t know what is,” said John Henneberger, a director of Texas Housers, an advocacy group that filed a lawsuit last week in Federal District Court to enforce the original HUD letter.
“Fountain View was kind of the last stand,” he said. “We spent eight or nine years documenting systematic and pervasive racial discrimination in Houston — it is an open-and-shut case.”
Mr. Brown, the HUD spokesman, said the agreement required the city to “put in place new procedures for the building of affordable housing” and a study on how to increase affordable housing in the city’s Galleria district, where Fountain View was to be built.
There are other signs of change within HUD that could make it far less likely that similar cases would ever be pursued.
Ms. Farías, according to six current department officials, has told HUD managers that she intends to replace her top subordinate, Timothy Smyth, who played a central role in the Houston case. Bryan Greene, another senior manager, will be reassigned as part of the shake-up, the officials said.
Mr. Brown, in an email, said no one had been reassigned yet — but he added that it was “well within the assistant secretary’s authority after 120 days to reassign senior-level personnel.”
Morale at the division is sinking. At a meeting this month of HUD regional housing directors in Atlanta, Ms. Farías — a former vice chairwoman of the Bexar County, Tex., Republicans and a Trump campaign supporter — told one of the directors that she preferred older HUD employees because they were more likely to have had experience working for Republican administrations.
Earlier, according to two aides who requested anonymity for fear of retribution, she had told her staff that it was her intention to root out people she viewed as “Obama plants.”
Ms. Farías, through a spokesman, denied making those statements.
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