WASHINGTON — The Justice Department sued Facebook on Thursday, accusing it of being un-American by favoring foreign workers with visas over those from the United States, in a new push against tech companies in the waning days of the Trump administration.

In the complaint, the department’s civil rights division said Facebook “refused to recruit, consider or hire qualified and available U.S. workers” for more than 2,600 positions, with an average salary of $156,000. Those jobs instead went to immigrant visa holders, according to the complaint.

The action followed a two-year investigation into whether Facebook intentionally favored so-called H1-B visa and other temporary immigrant workers over U.S. workers, the Justice Department said.

“Our message to workers is clear: If companies deny employment opportunities by illegally preferring temporary visa holders, the Department of Justice will hold them accountable,” said Eric S. Dreiband, the assistant attorney general for the civil rights division. “Our message to all employers — including those in the technology sector — is clear: You cannot illegally prefer to recruit, consider or hire temporary visa holders over U.S. workers.”

Andy Stone, a Facebook spokesman, said, “Facebook has been cooperating with the D.O.J. in its review of this issue, and while we dispute the allegations in the complaint, we cannot comment further on pending litigation.”

Bipartisan anger in Washington has mounted in recent years against Facebook, Google, Amazon and Apple — some of the world’s most valuable companies — for data privacy abuses, the spread of disinformation and other toxic content on their platforms, and complaints of anticompetitive practices that have harmed consumers and small businesses.

For months, regulators and lawmakers have homed in on Facebook for possible monopoly violations. The Federal Trade Commission and dozens of states are preparing antitrust lawsuits against the social network for maintaining its power through mergers of nascent competitors, such as Instagram and WhatsApp. They are expected to announce plans for legal action soon, people briefed on the cases have said.

The discrimination suit, which goes before an administrative law judge, opens a different front in Washington’s battle against Big Tech. Although President Trump has jabbed at the companies as recently as this week, when he threatened to revoke speech liability protections for internet platforms like Facebook and Twitter, it is the first time the administration has brought legal action claiming immigrant employment bias.

Skilled-worker visas in the technology industry have been a focus of debate for a decade. Facebook, Google, Microsoft, IBM and other companies have lobbied for years to expand H1-B visas, arguing the importance of getting the best engineers from overseas, particularly from China and India. Critics have called the visa program a crutch for tech companies to overlook U.S.-born talent and lure foreign workers at lower wages.

Mr. Trump has been a vocal critic of temporary worker visas. In October, his administration announced new rules for the H1-B program, substantially raising the wages that U.S. companies must pay foreign hires and narrowing eligibility criteria for applicants.

The Justice Department has rarely sued tech companies on the issue, though other agencies have accused the firms of racial or gender bias. In 2016, the Labor Department sued the data firm Palantir, alleging bias against Asians. The Labor Department separately sued Google to reveal data on hiring based on gender, race, religion and sexual orientation.

According to its complaint, the Justice Department found that between Jan. 1 and Sept. 18 last year, Facebook routinely put H1-B and other immigrant temporary workers on a track for permanent employment that was not available to U.S. citizens. Facebook also used less effective methods to advertise jobs to U.S. workers, including declining to promote the positions on Facebook.com/careers, the department said.

The hiring spotlighted by the complaint made up just 0.5 percent of Facebook’s 50,000 employees. But the Justice Department said Facebook had violated federal labor laws that require employers to make permanent employment opportunities as easily available to U.S. workers as they are to foreign visa holders.

“Facebook’s discriminatory recruitment and hiring practice is routine, ongoing and widespread,” the complaint said.

Mark Zuckerberg, the chief executive of Facebook, has for years made fighting for immigrants’ rights to work in the U.S. tech industry a pet issue. In 2013, he and several friends created Fwd.us, a nonprofit group that pushed for an overhaul of immigration laws and stumped for easing the immigration process for tech workers.

The issue has been a source of friction between Mr. Zuckerberg and Mr. Trump. In 2015, leaders at Fwd.us chafed at Mr. Trump’s immigration proposals, which would have restricted H-1B visas for skilled, foreign-born employees. They claimed that the plan would “radically restrict” paths to the United States for immigrant tech workers.

When Mr. Trump signed an executive order in 2017 limiting immigration from majority-Muslim countries, Mr. Zuckerberg spoke out against it.

“We need to keep this country safe, but we should do that by focusing on people who actually pose a threat,” he said in a post to his Facebook page. “We should also keep our doors open to refugees and those who need help. That’s who we are.”

Kim Clarke, a lawyer at Varnum who advises employers on immigration and labor issues, said the Justice Department suit could have a chilling effect on tech hiring.

“In the long run, if broader tech companies can’t hire the skilled talent on which they rely, their competitive positions will be hindered,” Ms. Clarke said. “The trickle-down effect of this action could impact even smaller employers that hire only a handful of foreign workers.”

Cecilia Kang reported from Washington, and Mike Isaac from San Francisco.