When Asher Lucas’s co-workers started taunting him for being transgender, saying he was “born a girl and needed to be a girl,” he figured this type of bullying would not be tolerated at a well-known restaurant.

But after complaining to his manager, Mr. Lucas was fired along with three employees who spoke up on his behalf.

“This cannot be legal,” Mr. Lucas remembers thinking when his boss told him in a voice mail message that he was fired.

The Equal Employment Opportunity Commission agreed with Mr. Lucas. In October, the agency sued his employer, Culver’s, in federal court in Michigan, saying the restaurant had engaged in unlawful employment practices by allowing co-workers to harass Mr. Lucas because “he is transgender and retaliating against those who opposed the harassment.”

But in the last several weeks, the E.E.O.C., the nation’s primary regulator focused on workplace discrimination, made an about-face in Mr. Lucas’s case and in several others involving transgender and nonbinary workers.

It moved to dismiss the case against Culver’s, arguing it could run afoul of President Trump’s executive order asserting that there are only two sexes, male and female.

Citing that order, the E.E.O.C. also asked judges to dismiss six other lawsuits the agency had brought that accused a range of companies, from a pizzeria at Chicago O’Hare International Airport to a hotel franchise in western New York, of subjecting transgender and nonbinary workers to hostile work environments and then often firing them when they complained.

A spokesman for the E.E.O.C. declined to comment. A lawyer for Culver’s did not respond to requests for comment.

The stark reversals come just weeks after Mr. Trump, who has signed five executive orders targeting transgender rights, shook up the E.E.O.C. He fired two of its Democratic commissioners, along with its general counsel, and he appointed Andrea Lucas as acting chair.

Established by Congress roughly 60 years ago, the E.E.O.C. enforces anti-discrimination laws in the workplace, including Title VII of the 1964 Civil Rights Act, which says that employers cannot discriminate against workers based on race, color, religion, national origin or sex.

While the transgender and nonbinary workers may find other legal recourse, such as hiring a lawyer to sue their employers on their own, the E.E.O.C.’s reversal on gender-identity cases is a major departure in how the federal agency protects civil rights.

The shift has left workers like Mr. Lucas feeling betrayed and many of the agency’s staff despairing.

“We filed these cases because there was strong evidence of discrimination based on existing law, and the president’s executive order does not change that,” said Karla Gilbride, who was the general counsel of the E.E.O.C. until she was fired in January.

She added that “walking away from these cases and these individuals who put their trust in us is a betrayal.”

That sentiment has been spreading throughout the agency, according to more than a dozen current employees, who spoke on the condition of anonymity for fear of losing their jobs. Some of the lawyers who had originally filed the cases refused to sign the motions to dismiss, five of the employees said.

One current judge was so upset that she decided to speak out.

“I am ashamed at how this agency, which I so believed in, is abandoning some of the most vulnerable people in our society,” Karen Ortiz, an administrative judge in the E.E.O.C.’s New York district office, said in an interview.

Judge Ortiz, who hears discrimination claims brought by employees of the federal government, says she knows that speaking out could cost her job, but she is willing to take the risk.

In recent weeks, supervisors have demanded that judges like Judge Ortiz pause evaluating cases involving employees who believe they have been discriminated against on the basis of their gender identity. The agency has also paused investigating new complaints from workers on that same basis, according to the employees.

It is not clear how many complaints are on hold, but last year, the agency received more than 3,000 charges of discrimination based on sexual orientation or gender identity, up more than 38 percent from two years earlier.

The E.E.O.C. receives tens of thousands of complaints each year, but chooses to bring its own lawsuits in less than 1 percent of them, agency statistics show. That means that the lawsuits, including the half-dozen the agency is trying to dismiss, are scrutinized at multiple levels and reflect the most serious cases of discrimination.

Among the cases that the E.E.O.C. has moved to drop in recent weeks is a lawsuit against a major cosmetics company on behalf of Emma Robertson and other nonbinary employees who worked in a Santa Clara, Calif., store.

Lush, their employer, created a hostile work environment for Ms. Robertson and her colleagues, the lawsuit said. Ms. Robertson, who uses she/her pronouns, said her manager had berated her for not being “gay enough,” calling her a bitch and commenting on her body.

Ms. Robertson, in an interview, said she was devastated. “I had thought this company was so magical, and so this felt like being betrayed by someone I loved,” she said. Ms. Robertson said she had started showing up early for work so she could cry alone in her car.

The store manager also harassed another nonbinary employee, according to the lawsuit, grabbing the worker’s “buttocks approximately five times.” Ms. Robertson and other employees complained, the lawsuit said, but Lush failed to stop the harassment.

“Lush has always complied with all of the civil rights laws and denies the allegations contained in the complaint filed by the Equal Employment Opportunity Commission,” a Lush spokeswoman said.

When the E.E.O.C. filed suit on her behalf in September, Ms. Robertson said, she truly felt “seen” for who she was and what she went through.

The agency’s reversal felt like a gut punch.

“I had spent so much time fighting and reliving what happened to me,” she said. “It all felt pointless.”

Cases like Ms. Robertson’s used to be a major focus for the agency.

In 2023, protecting L.G.B.T.Q. workers was highlighted in the E.E.O.C.’s multiyear strategic plan outlining the agency’s top enforcement priorities.

Last year, it also updated its guidance to employers: Deliberately referring to workers by the wrong pronouns or barring their access to bathrooms that corresponded with their gender identity could constitute harassment, the agency said.

That came after the Supreme Court ruled in 2020 that gay and transgender workers are protected from workplace discrimination under the landmark civil rights law. “An employer who fires an individual merely for being gay or transgender defies the law,” Justice Neil M. Gorsuch, who was nominated by Mr. Trump, wrote for the majority in a 6-to-3 opinion.

Now the agency is aggressively moving in another direction. In January, Ms. Lucas, the acting chair, blasted the E.E.O.C.’s harassment guidance as “fundamentally flawed.” Sex is “binary,” she said, and it is “not harassment to acknowledge these truths — or to use language like pronouns that flow from these realities.”

She has positioned herself as a partner to the Trump administration, as it works to reshape how the federal government and American society more broadly treat transgender and nonbinary people.

Mr. Trump has issued a spate of executive orders targeting transgender rights, including one that withdraws federal funds to schools that allow transgender women and girls to compete in women’s sports and another that authorizes the Defense Department to potentially bar transgender soldiers from military service.

Anna Kelly, a White House spokeswoman, said, “President Trump’s entire administration is aligned with his overwhelmingly popular agenda to end radical and wasteful D.E.I. policies.”

At the E.E.O.C., Judge Ortiz is choosing to ignore the guidance from her bosses.

Obeying, she said in an interview, sets a dangerous precedent.

“Imagine if the president declared that there was just one race in America and that race was white,” Judge Ortiz said. “Then would federal agencies just permit discrimination against everyone else?”

Shortly after receiving an email from a supervisor about the pivot on gender-identity cases, Judge Ortiz shot back one of her own, calling on Ms. Lucas to resign.

“I will not compromise my ethics and my duty to uphold the law,” Judge Ortiz wrote in an agencywide email, which was reviewed by The New York Times.

She also filed a complaint about Ms. Lucas with the D.C. Bar, writing that it was illegal to “direct E.E.O.C. employees to withdraw” from litigation, according to a copy of the complaint reviewed by The Times.

Mr. Lucas, the transgender man, said he planned to pursue his case with a private lawyer, but was more worried for the broader community of transgender people.

“It feels like the government is trying to erase trans people and make it so you can discriminate against us and harass us,” Mr. Lucas said. “These people were fighting with me and for me, and now they aren’t.”

Matthew Goldstein contributed reporting. Susan C. Beachy contributed research.