WASHINGTON — As racial justice protests erupted nationwide last year, President Donald J. Trump, struggling to find a winning campaign theme, hit on a message that he stressed over and over: The real domestic threat to the United States emanated from the radical left, even though law enforcement authorities had long since concluded it came from the far right.

It was a message that was quickly embraced and amplified by his attorney general and his top homeland security officials, who translated it into a shift in criminal justice and national security priorities even as Mr. Trump was beginning to openly stoke the outrage that months later would culminate in the storming of the Capitol by right-wing extremists.

Mr. Trump’s efforts to focus his administration on the antifa movement and leftist groups did not stop the Justice Department and the F.B.I. from pursuing cases of right-wing extremism. They broke up a kidnapping plot, for example, targeting Gov. Gretchen Whitmer of Michigan, a Democrat.

But the effect of his direction was nonetheless substantial, according to interviews with current and former officials, diverting key portions of the federal law enforcement and domestic security agencies at a time when the threat from the far right was building ominously.

• In late spring and early summer, as the racial justice demonstrations intensified, Justice Department officials began shifting federal prosecutors and F.B.I. agents from investigations into violent white supremacists to focus on cases involving rioters or anarchists, including those who might be associated with the antifa movement. One Justice Department prosecutor was sufficiently concerned about an excessive focus on antifa that the official went to the department’s independent inspector general, Michael E. Horowitz, telling his office that politics might have played a part.

• Federal prosecutors and agents felt pressure to uncover a left-wing extremist criminal conspiracy that never materialized, according to two people who worked on Justice Department efforts to counter domestic terrorism. They were told to do so even though the F.B.I., in particular, had increasingly expressed concern about the threat from white supremacists, long the top domestic terrorism threat, and well-organized far-right extremist groups that had allied themselves with the president.

• White House and Justice Department officials stifled internal efforts to publicly promote concerns about the far-right threat, with aides to Mr. Trump seeking to suppress the phrase “domestic terrorism” in internal discussions, according to a former official at the Department of Homeland Security.

• Requests for funding to bolster the number of analysts who search social media posts for warnings of potential violent extremism were denied by top homeland security officials, limiting the department’s ability to spot developing threats like the post-Election Day anger among far-right groups over Mr. Trump’s loss.

The scale and intensity of the threat developing on the right became stunningly clear on Jan. 6, when news broadcasts and social media were flooded with images of far-right militias, followers of the QAnon conspiracy movement and white supremacists storming the Capitol.

Militias and other dangerous elements of the far right saw “an ally in the White House,” said Mary McCord, a former Justice Department official who teaches at Georgetown University and focuses on domestic terrorism. “That has, I think, allowed them to grow and recruit and try to mainstream their opinions, which is why I think you end up seeing what we saw” at the Capitol.

A Focus on ‘Anarchists and Thugs’

Mr. Trump’s focus on what he portrayed as a major threat from antifa was embraced in particular by Attorney General William P. Barr.

Mr. Barr had long harbored concerns about protests and violence from the left. Soon after taking office in early 2019, he began a weekly national security briefing by asking the F.B.I. what it was doing to combat antifa, according to two people briefed on the meetings. Officials viewed his sense of the threat as exaggerated. They explained that it was not a terrorist organization, but rather a loose movement without an organization or hierarchy, and tried to correct what they described as misperceptions, according to one of the people.

Still, in meetings last year with political appointees in Washington, department investigators felt pressured to find evidence that antifa adherents were conspiring to conduct coordinated terrorist attacks.

When F.B.I. intelligence continued to deem white nationalists the leading domestic terrorism threats — part of what the bureau describes as racially or ethnically motivated violent extremists — prosecutors were asked to also consider information from the Department of Homeland Security that antifa and radical leftist anarchists were instead the leading threats, according to a person involved in the conversations.

Mr. Barr said in a statement that “there was no ‘prioritization’” of the leftist threat, and that all violence should be condemned.

“The F.B.I. already had a robust program to combat violence driven by white supremacy and nationalism,” Mr. Barr said. “I wanted there to be a comparable one for antifa and antifalike groups.”

The pressure from Mr. Trump was unrelenting. After Christopher A. Wray, the F.B.I. director, testified to Congress in September that antifa was “more of an ideology or a movement than an organization,” Mr. Trump lashed out at him on Twitter, saying that the F.B.I. protected such “anarchists and thugs” and allowed them “to get away with ‘murder.’”

Investigators at the Justice Department and the Department of Homeland Security moved quickly and forcefully to address the violence that erupted amid the summer’s racial justice protests.

The demonstrations gave way to looting and rioting, including serious injuries and shootings. Over several chaotic nights in Minneapolis, rioters burned down a corridor of largely immigrant-owned businesses and set a police precinct on fire. Similar scenes played out in other cities.

In late August, Michael Reinoehl, a self-professed antifa supporter, shot and killed a pro-Trump protester in Portland, Ore. The president cheered his death at the hands of the federal officers who later tried to apprehend him. “We got him,” he said.

But while Mr. Trump and others saw the developments as evidence of a major assault from the left, the picture was actually more complicated.

The shooting by Mr. Reinoehl, as the F.B.I. pointed out this month in an internal memo, was the first killing in more than 20 years by what the bureau classifies as an “anarchist violent extremist,” the type of threat Mr. Trump had emphasized.

Over the late spring and summer, the F.B.I. opened more than 400 domestic terrorism investigations, including about 40 cases into possible antifa adherents and 40 into the boogaloo, a right-wing movement seeking to start a civil war, along with investigations into white supremacists suspected of menacing protesters, according to F.B.I. data and a former Justice Department official. Even among those movements, career prosecutors saw the boogaloo as the gravest threat.

Members of violent militias began to go to protests as self-appointed police forces, sometimes saying that they had heeded Mr. Trump’s call. They attended Republican events as self-described security forces.

Still, Justice Department leadership was adamant that terrorism investigators focus on antifa as the demonstrations spread, according to an official who worked on the inquiries.

The small cadre of intelligence analysts inside the department’s counterterrorism section were pulled into the effort, writing twice daily reports. National security prosecutors staffed command posts at the F.B.I. to deal with the protests and associated violence and property crimes, and to help protect statues and monuments seen as potential targets.

All of this was a strain on the counterterrorism section, which has only a few dozen prosecutors and like other parts of the department was reeling from the coronavirus. A top F.B.I. domestic terrorism chief also expressed concern to Justice Department officials over the summer about the diversion of resources.

The counterterrorism section at the time was working with prosecutors and agents around the country on cases involving people affiliated with the Three Percenters, Oath Keepers, other militia members and violent white supremacists. In some parts of the country, agents who had been investigating violent white supremacists pivoted to investigate anarchists and others involved in the rioting, struggling in certain cases to find any conspiracy or other federal charges to bring against them.

Around the same time, the F.B.I. was tracking worrisome threats emanating from the far right. Agents in Michigan monitoring members of a violent antigovernment militia called Wolverine Watchmen received intelligence in June that the men planned to recruit more members and kidnap state governors, according to court documents.

After six members of the group were charged in October with plotting to abduct Ms. Whitmer, one of Mr. Trump’s most vocal opponents, the president insulted her and reiterated that the left posed the true threat. “She calls me a White Supremacist — while Biden and Democrats refuse to condemn Antifa, Anarchists, Looters and Mobs that burn down Democrat run cities,” Mr. Trump said on Twitter.

Dozens of F.B.I. employees and senior managers were sent on temporary assignments to Portland — including the head of the Tampa field office, who was an expert in Islamic terrorism, according to current and former law enforcement officials — where left-leaning protests had intensified since tactical federal teams arrived.

Some F.B.I. agents and Justice Department officials expressed concern that the Portland work was a drain on the bureau’s effort to combat what they viewed as the more lethal strains of domestic extremism. The bureau had about 1,000 domestic terrorism cases under investigation at the time, and only several hundred agents in the field assigned to them. The Homeland Security Department even sent agents to Portland who were usually assigned to investigate drug cartels at the border.

Mr. Barr also formed a task force run by trusted U.S. attorneys in Texas and New Jersey to prosecute antigovernment extremists. Terrorism prosecutors working on the investigations arising from the summer’s violence were not told beforehand of Mr. Barr’s decision. They questioned the rationale behind the task force because it seemed to duplicate their work and could create confusion, according to two people familiar with their pushback.

Ultimately, the federal response to last year’s protests elicited a mixed bag. Federal prosecutors nationwide charged more than 200 people with crimes, including some who self-identified with antifa.

But the F.B.I. also charged adherents of the boogaloo, including an Air Force sergeant suspected of murdering a federal officer and trying to kill another in California. The sergeant had previously been charged with the shooting death of a sheriff’s deputy in Santa Cruz County during a gun battle on June 6 that led to his arrest.

The Homeland Threat

Domestic terrorism has long been a politically sensitive issue for the Department of Homeland Security.

A warning in a 2009 homeland security report that military veterans returning from combat could be vulnerable for recruitment by terrorist groups or extremists prompted backlash from conservatives, forcing the homeland security secretary at the time, Janet Napolitano, to apologize and retract the report. An edited version was eventually issued, but the lesson about the political risks of highlighting far-right extremism lingered inside the department.

“They overhype the threat of the far left at the expense of far-right extremism,” said Daryl Johnson, a former senior analyst at the department who wrote the 2009 report.

Like Mr. Barr, Mr. Trump’s acting homeland security secretary, Chad F. Wolf, took his lead from the White House and emphasized the threat from antifa. At one point, Mr. Wolf formed a task force that deployed tactical agents to protect statues and monuments.

Mr. Wolf denied that the administration’s response to the violence at racial justice protests came at the cost of efforts to combat far-right violence, noting that the agency affirmed the rising threat of white supremacy in an assessment in 2019.

“You could argue the reverse. The fact we were focused on white supremacist extremists in late 2019, early ’20, we missed the antifa stuff coming up,” Mr. Wolf said. “One could always go back and say, ‘You focused on this at the expense of that.’ I would say we focused on things happening in real time.”

Mr. Trump said in May that he intended to designate antifa a domestic terrorist organization. National Security Council staff members, including Andrew Veprek, an ally of Stephen Miller who is now at the State Department, asked homeland security officials for evidence to justify such a designation. They sought information about possible ties between antifa and foreign entities; federal law defines domestic terrorism but the statute does not carry any criminal penalties, and designations of terrorist organizations are limited to foreign groups.

In fact, the F.B.I. had seen troubling evidence of white supremacists in the United States with foreign ties, including one group that agents believe was being directed by an American living in Russia. The group, called the Base, was such a severe threat that the F.B.I. briefed Mr. Barr about it.

Homeland security officials balked at helping designate antifa as a terrorist organization, and the effort failed.

Officials in the department’s Office of Intelligence and Analysis also expressed concern after Mr. Wolf questioned one of their reports that labeled the boogaloo as “far right” in describing the shooting death of the federal officer in which the suspect, an Air Force sergeant, was linked to the movement. Asked about his response, Mr. Wolf said he was only trying to gain information, not alter reports.

Under the Trump administration, analysts in the intelligence and analysis office had even more incentive to produce reports on threats outside of right-wing extremism, said Elizabeth Neumann, the former assistant homeland security secretary for counterterrorism and threat prevention under Mr. Trump.

Many viewed their performance reviews as tied to whether they produced reports that aligned with the Trump administration’s priorities, including Mexican cartel organizations, foreign terrorism and antifa, rather than reports on militias and white supremacists. The number of warnings about all types of extremists in the second half of last year eventually dwindled, according to current and former officials.

“You can read the tea leaves and say domestic terrorism isn’t going to be our priority,” Ms. Neumann said.

“The culture absorbs those messages they hear the president speak or tweet,” she said, adding that some White House officials even cautioned against using the phrase “domestic terrorism.”

Last spring, Brian Murphy, then the homeland security intelligence chief, requested $14 million to bolster training and increase staff to analyze social media for extremist threats, given that online forums had become a prime recruiting and organizing ground.

Mr. Wolf’s deputy, Kenneth T. Cuccinelli II, rejected the request, as well as an appeal for $8 million, officials said.

Mr. Cuccinelli said in a statement that requests for additional funding would have come at the expense of other parts of the agency. He added that he had been working to shift resources from other parts of the department to expand training for the intelligence branch.

Mr. Murphy had filed a whistle-blower complaint in September that prompted an outcry. He accused department leaders of ordering him to modify intelligence assessments to make the threat of white supremacy “appear less severe” and include information on violent “left-wing” groups and antifa. Mr. Wolf and Mr. Cuccinelli have denied the allegations, and after congressional backlash, they eventually released a report in October identifying white supremacy as the “most persistent and lethal threat” in the United States.

Antifa Until the End

Campaigning for re-election, Mr. Trump spent the summer blaming rioting and violence on Democratic governors and mayors and warning about a “left-wing cultural revolution.”

Armed far-right militia groups started appearing at racial justice protests and demonstrations about the outcome of the election. Extremists groups like the Proud Boys marched in Washington in December, clashing with anti-Trump protesters in altercations that included stabbings.

The Homeland Security Department’s intelligence branch issued an assessment on Dec. 30 highlighting the potential for white supremacists to carry out “mass casualty” attacks, according to a copy obtained by The New York Times.

But there was no specific mention of armed groups targeting the Capitol, despite plenty of indicators online. The acting chief of the Capitol Police, Yogananda D. Pittman, later said that the department knew militias and white supremacists would be coming and “that there was a strong potential for violence and that Congress was the target.”

In the days before Jan. 6, the Secret Service was told by homeland security officials to expect only an “elevated threat environment,” according to people familiar with the meeting.

The Trump administration, however, continued to play up the threat of antifa. The night before the assault on the Capitol, the White House issued a memo seeking to bar any foreigners affiliated with antifa from entering the country and, once again, try to determine if the movement could be classified as a terrorist organization.

When the pro-Trump mob stormed the Capitol, some shouted explicit chants against antifa. Others were captured on video yelling, “We were invited by the president of the United States.”

Mike Baker and John Eligon contributed reporting.