WASHINGTON — The Department of Homeland Security warned on Tuesday that violent white supremacy was the “most persistent and lethal threat in the homeland” in an annual assessment that a former intelligence chief had accused the agency of withholding in deference to President Trump.

The intelligence chief-turned-whistle-blower last month accused the department of blocking the report and directing analysts to play down the threat of violent white racism as well as Russian election interference to align the agency’s message with the president’s. But the final report appeared to do no such thing.

The threat assessment highlighted white supremacists as the most deadly among domestic terrorists in recent years and Russia as the primary threat to spreading disinformation.

“I am particularly concerned about white supremacist violent extremists who have been exceptionally lethal in their abhorrent, targeted attacks in recent years,” Chad F. Wolf, the acting secretary of homeland security, wrote in the foreward to the assessment. The threat report also stated that “Russia is the likely primary covert influence actor and purveyor of disinformation and misinformation within the homeland.”

The agency also highlighted Iran and China’s cyberwarfare abilities and warned of a potential surge in migration to the southwest border.

The delayed release of the report has been a point of scrutiny for a department that has faced consistent accusations of morphing into a tool for Mr. Trump’s re-election campaign. After the department singled out domestic terrorists and specifically white supremacists in a terrorism framework in September 2019, the agency’s leadership committed to releasing a follow-up assessment to the threat as well as a blueprint to confront it within months. It took far longer.

Brian Murphy, who was demoted from his post as the Homeland Security Department’s intelligence chief in August, said last month in a whistle-blower complaint that Mr. Wolf and his deputy, Kenneth T. Cuccinelli, blocked the release of the assessment because of how it would “reflect upon President Trump.”

The Homeland Security blueprint did finally emerge, shortly after Mr. Murphy’s complaint. It included $10 million for nonprofits and other organizations to prevent extremist violence.

The administration’s treatment of white supremacy re-emerged as an issue last week, when Mr. Trump failed to condemn white racist violence during the presidential debate.

Now, the Homeland Security Department has done so in the assessment.

“This threat assessment confirms two things: that white supremacist extremists are the top domestic threat to the homeland, and they are often inspired by President Trump’s rhetoric,” said Representative Bennie Thompson, Democrat of Mississippi and the chairman of the House Homeland Security Committee.

The threat assessment for the most part mirrored drafts that were leaked to the public, refuting concerns that the department would dilute any warnings. The department did add a section absent from previous versions of the report, titled “exploitation of lawful and protected speech and protests.”

The section echoed Mr. Trump’s description of city governments led by Democrats as fostering chaos.

“We have seen over 100 days of violence and destruction in our cities,” according to the report. “The co-opting of lawful protests led to destruction of government property and have turned deadly.”

While a majority of the protests against police violence and racism this summer were peaceful, some did include individuals who committed violent acts, including in Portland, Ore., where the Homeland Security Department sent teams of tactical agents. The aggressive methods of those agents, including forcing demonstrators into unmarked cars and using tear gas, is under investigation by the inspectors general for the Homeland Security and Justice Departments.

Some demonstrators also lobbed commercial-grade fireworks at a federal courthouse and the agents surrounding it. A self-proclaimed supporter of the loose-knit movement known as antifa was also accused of fatally shooting a right-wing activist who was part of a pro-Trump caravan in Portland. That antifa supporter, Michael Forest Reinoehl, was shot and killed last month by law enforcement agents before he could be taken into custody.

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While the threat assessment does not specifically mention antifa, it does warn of anti-government groups that could commit violence under the guise of protests. Last May, a suspected member of the boogaloo, a generally right-wing movement that seeks to bring about a second civil war, shot and killed a member of the Federal Protective Service during protests in Oakland, Calif. Mr. Trump blamed “the left” for the killing.

The report also warns that extremist groups could be inspired to attack because of restrictions to limit the spread of the coronavirus.

“We also remain particularly concerned about the impacts from Covid-19, where anti-government and anti-authority violent extremists could be motivated to conduct attacks in response to perceived infringement of liberties and government overreach,” the report said.

It also indicated that the department was preparing for an increase in migration to the southwestern border. Homeland security analysts warned that the easing of coronavirus restrictions could lead to an increase in border crossings by land and sea.

The department has cited the pandemic in using a public health emergency to seal the border to migrants, rapidly returning most to Mexico or other countries without offering to review their asylum claims.

In an interview with CBS published on Monday, Mr. Wolf defended the assessment, noting that the Russia threat was mentioned multiple times. But he also asserted that “the most long-term strategic threat to Americans, to the homeland and really to our way of life would be the threat from China,” a position that mirrors Mr. Trump’s.

Analysts described China as exploiting shortages of critical supplies, committing intellectual property theft and waging disinformation campaigns on the internet. As for election interference, China and Iran have for the most part targeted Mr. Trump, but intelligence officers have said that Russia presented a more severe short-term threat.

Javed Ali, a former senior director at the National Security Council under Mr. Trump, said the homeland threat assessment was reassuring “given the significant politicization that has occurred” in the Homeland Security Department.

“It was good to see the H.T.A. take a more objective, nonpartisan and analytically driven perspective on cataloging the major homeland threats,” Mr. Ali said, referring to the assessment.

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