WASHINGTON — Top officials with the Department of Homeland Security directed agency analysts to downplay threats from violent white supremacy and Russian election interference, a Homeland Security intelligence official said in a whistleblower complaint released on Wednesday.

Brian Murphy, the former head of the Homeland Security Department’s intelligence branch, said in the complaint that he was ordered this spring by Chad F. Wolf, the acting secretary of the department, to stop producing assessments on Russian interference and focus instead on Iran and China. That request, Murphy said, was routed through Wolf from Robert C. O’Brien, the White House national security adviser.

Wolf later told him not to disseminate a report on a Russian disinformation campaign to denigrate Joe Biden’s mental health because it “made the president look bad,” said Murphy, who warned that the actions in their totality threatened national security.

In other instances, the department’s second-highest ranked official, Kenneth T. Cuccinelli II, ordered Murphy to modify intelligence assessments to make the threat of white supremacy “appear less severe” and include information on violent “left-wing” groups and antifa, according to the complaint, which was filed on Tuesday but released Wednesday by the House Intelligence Committee.

In Murphy’s account, the two top officials at the department — both appointees of President Donald Trump who have not yet been confirmed by the Senate for their positions — appeared to shape the agency’s views around the president’s language and political interests in ways that stretched the law and their authority.Trump has ignored or downplayed Russian election interference since 2016, when the U.S. intelligence community agreed that Moscow had intervened to help elect him, a declaration that he feared would undermine his legitimacy. And the president has always been reluctant to shun or criticize groups that have supported him, including white supremacists and supporters of the QAnon conspiracy theory. That reluctance has dovetailed with his current desire to focus voter attention on unrest in cities, that has been fomented by the Black Lives Matter movement.

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And while Trump’s distaste for the intelligence agencies is not new, Murphy’s complaint provided some of the most graphic claims yet that career, nonpartisan analysts had been muzzled or shoved aside to downplay the threat posed specifically by Russia as it sought to sow discord and bolster Trump’s reelection campaign.

Murphy was demoted from his post in August to the Homeland Security Department’s management division after his office compiled intelligence reports on protesters and journalists in Portland, Oregon. But he asserted in the complaint that his real offense was raising concerns to superiors about the directions he was given and for cooperating with the department’s inspector general. He asked the inspector general to investigate and reinstate him as the intelligence chief.

“Mr. Murphy followed proper, lawful whistleblower rules in reporting serious allegations of misconduct against DHS leadership, particularly involving political distortion of intelligence analysis and retaliation,” Mark S. Zaid, Murphy’s lawyer, said in a statement.

Democrats on the House Intelligence Committee asked Murphy to testify in private on Sept. 21, a possible precursor to a public hearing in the weeks before Election Day.

“We will get to the bottom of this, expose any and all misconduct or corruption to the American people, and put a stop to the politicization of intelligence,” said Rep. Adam B. Schiff, D-Calif. and the chairperson of the committee. He said the allegations of politically censored intelligence assessments were particularly worrisome in light of the Trump administration’s decision last month to stop briefing lawmakers in person on election security threats.

Sarah Matthews, a White House spokeswoman, said in a statement that O’Brien had “never sought to dictate the intelligence community’s focus on threats to the integrity of our elections or on any other topic.” She called Murphy a “disgruntled former employee” whom O’Brien had never heard of. But, she added, the national security adviser “consistently and publicly advocated for a holistic focus on all threats to our elections — whether from Russia, Iran, China or any other malign actor.”

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Alexei Woltornist, the spokesman for the Homeland Security Department, rejected Murphy’s allegations.

“We flatly deny that there is any truth to the merits of Mr. Murphy’s claim,” Woltornist said. “DHS looks forward to the results of any resulting investigation, and we expect it will conclude that no retaliatory action was taken against Mr. Murphy.”

As president, Trump has clashed frequently with the intelligence community, particularly over the issue of election interference. At a news conference in 2018 in Helsinki, Trump sided with President Vladimir Putin of Russia and said he did not think Moscow was responsible for the 2016 interference. A few months later, Trump dismissed the CIA’s assessment that the Saudi crown prince was responsible for the murder of Jamal Khashoggi, a prominent Washington Post columnist. In February 2019, after intelligence chiefs offered Congress assessments on North Korea and Iran that were at odds with the White House, the president told them to “go back to school.”

Trump and his allies have also dismissed members of the intelligence community as overstating Russian espionage to undermine his presidency.

In his roles as a senior analyst and then the top intelligence official at the Homeland Security Department, Murphy was responsible for producing regular updates for the FBI, state election authorities and law enforcement on threats to U.S. elections by foreign powers.

In May, he said, Wolf directed him to stop providing assessments of the Russian threat, which favored Trump’s reelection, and instead focus on the activities of China and Iran, two other states that intelligence analysts have said pose a possible threat to the election and oppose Trump. China and Iran have so far not taken the kind of active measures that Moscow has, intelligence analysts say.

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Murphy said he refused to comply, “as doing so would put the country in substantial and specific danger.”

Two months later, in July, Wolf again approached Murphy and asked him to hold back a warning that Russia was mounting a disinformation campaign around Biden’s mental health. That report also noted that China and Iran were criticizing Trump’s health.Murphy again objected, saying it was “improper” to hold back intelligence because of “political embarrassment.” This time, the complaint said, he was pushed out of the decision-making process. A modified report was later leaked to the news media equating Russia’s actions with those of China and Iran “in a manner that is misleading and inconsistent with the actual intelligence data,” the complaint said.

Andrew Bates, a spokesman for Biden, said that the claims, if true, “cement a pattern of high-ranking Trump administration officials not only keeping law enforcement officials and the American people in the dark about assaults on our democracy, but corrupting intelligence processes to benefit the president politically.”

Murphy also claimed that in a meeting in December, Cuccinelli asked him to alter intelligence reports “outlining high levels of corruption, violence and poor economic conditions” in Honduras, Guatemala and El Salvador. The reports are used to inform officers who assess claims from migrants seeking asylum.

Murphy said Cuccinelli was deeply unsatisfied with the reports and accused “unknown deep state intelligence analysts” of compiling the intelligence information to undermine Trump’s objective of restricting asylum at the border.

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By Murphy’s account, Cuccinelli then ordered him and David J. Glawe, the department’s top intelligence official before Murphy, to produce names of “deep state” employees who put together the reports so they could be fired or reassigned. Murphy said he viewed the direction as illegal and an abuse of Cuccinelli’s authority, and he refused to carry it out.

Cuccinelli and Wolf also blocked the release of a threat assessment completed in March by Murphy’s office that would have singled out white supremacy and Russian election interference as pressing dangers to the United States, according to the complaint. Murphy said Glawe was told the release of the report would be blocked because of how it would “reflect upon President Trump.”A year ago, Kevin K. McAleenan, then the acting secretary of Homeland Security, promised the department would release the threat assessment, along with a blueprint of how to combat white nationalism and domestic terrorism.

After Glawe retired, Murphy met with Cuccinelli in May and June to ask about the release of the assessment.

“Mr. Cuccinelli stated that Mr. Murphy needed to specifically modify the section on white supremacy in a manner that made the threat appear less severe, as well as include information on the prominence of violent ‘left-wing’ groups,” according to the report. Murphy said that he had declined to make the modifications and that they constituted censorship.

Murphy again pushed for the release of the report on July 8 in a meeting with Wolf and his deputy chief of staff, Scott Erickson, the complaint states. Wolf repeated Cuccinelli’s complaints and asked that the threat analysis include information on the unrest in Portland, Oregon. Murphy said he did not agree with edits that undermined the gathered intelligence.

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Murphy said in the report that the final version of the assessment would be altered to emphasize “anarchist” groups and antifa, a loose collection of left-wing anti-fascist activists that former Homeland Security analysts had determined to be not as deadly as more organized white nationalists.

During meetings in May and July, Cuccinelli and Wolf directed Murphy to change other intelligence briefings that were shared with federal and state law enforcement agencies to ensure that they matched Trump’s descriptions of the danger posed by antifa.

The allegations from Murphy are only the latest to hit the Homeland Security Department, which was originally built to protect the United States from foreign terrorism and improve responses to national emergencies. Wolf’s deployment of teams of tactical agents to Portland prompted widespread criticism from former Homeland Security officials and members of Congress that the agency, which is also responsible for carrying out most of Trump’s immigration policies, had become a tool for the president’s reelection campaign.

But Murphy has also been the subject of scrutiny at both the Homeland Security Department and the FBI.

He was reassigned by Wolf after his office distributed intelligence bulletins that partly targeted The New York Times for publishing an analysis indicating that the Homeland Security Department had little understanding of the situation in Portland when it deployed teams of tactical agents in camouflage to face crowds of protesters. Murphy said in the complaint that his office did not conduct surveillance of reporters’ private data but rather included their social media posts in the bulletins.

The analysis also summarized the tweets of Benjamin Wittes, the editor-in-chief of the blog Lawfare, including one that had showed an email from Murphy telling intelligence officers to refer to individuals attacking the federal courthouse in Portland as “VIOLENT ANTIFA ANARCHISTS.”

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“It is certainly possible that Murphy could have been a bad actor in some respects, which I think he clearly was, but also put out legitimate claims as a whistleblower,” Wittes said. “It’s also possible that he is protecting himself by making allegations.”Hours before the release of Murphy’s complaint, Wolf gave an annual address to summarize the work of the Homeland Security Department that was emblematic of the agency’s changing priorities under the Trump administration.

He blamed China and the World Health Organization for the coronavirus pandemic and local city and state officials for the unrest in Portland, while promoting the construction of Trump’s Southwest border wall. Wolf also touched on the department’s efforts to counter domestic extremism.

“Let me be clear: DHS stands in absolute opposition to any form of violent extremism, whether by white supremacists or anarchist extremists,” he told the audience.

Wolf added that the agency would issue the delayed plan for preventing extremist violence this week, although the department did not respond to inquiries of when it would be made public.