WASHINGTON — Well before his move to the Department of Homeland Security, Brian Murphy had become known as an ambitious counterterrorism investigator at the F.B.I., determined and relentless. At times, though, colleagues chafed at what some saw as an overzealous disregard for bureaucratic rules.
All of those traits may have been at play this week when Mr. Murphy, a career law enforcement officer, became a whistle-blower.
The Department of Homeland Security was built after the attacks of Sept. 11, 2001, 19 years ago Friday, to keep federal, state and local governments coordinated on national security threats. But in his whistle-blower complaint, Mr. Murphy, the department’s former intelligence chief, said its senior leaders directed him to do the opposite: play down the primary national security threats of white supremacy and Russian election interference, thus distorting intelligence to mirror President Trump’s messaging.
The allegations, coming less than two months before Election Day, add to the growing evidence that Mr. Trump has prioritized his own political goals over the word of his intelligence officials, and that the Homeland Security Department has become an instrument of his personal will. Mr. Murphy’s complaint reflects the current turmoil at homeland security and is another front in Mr. Trump’s battle with the government’s intelligence agencies.
The allegations also add to Mr. Murphy’s reputation. “Could he be a bit of a bull in a china shop? Absolutely,” said Kerry Sleeper, a former assistant director of the F.B.I. who once supervised Mr. Murphy. “But also that’s a person that allows change to happen.”
Mr. Murphy is not the first high-ranking official at the agency to rebel. A former chief of staff for the department, Miles Taylor, and a top counterterrorism analyst, Elizabeth Neumann, have also emerged as sharp voices of dissent after claiming the White House did not take the threat of white nationalism seriously, even after analysts found that such racists were significantly more deadly than far-left groups.
After close of business on Friday, the department also issued a “public action plan” detailing steps it would take to prevent terrorism, nearly a year after the agency singled out violent white supremacy as a primary national security threat and committed to releasing the blueprint to prevent it. The plan describes combating violent extremists groups but does not specifically mention white supremacist violence.
Mr. Murphy is still at the department, even after Chad F. Wolf, the acting secretary of homeland security, demoted him when reports emerged that his office made note of American journalists who had published leaked documents — including them in intelligence briefings his office shared with law enforcement agencies.
Mr. Murphy said in the whistle-blower complaint that the demotion was retaliation for his clashes with Mr. Wolf over what he asserted were efforts to warp intelligence reports.
“Why did D.H.S. come into existence? It came in to share information that state and local partners weren’t getting,” said Chuck Wexler, the executive director of the Police Executive Research Forum, a law enforcement policy organization. “It filled a void that didn’t exist. So if you start to filter that information, we’re back to square one.”
Mr. Murphy is currently preparing for interviews about the intelligence office with the inspector general of the Homeland Security Department and the House Intelligence Committee. The committee has been investigating the department’s intelligence branch since July after the office authorized analysts to collect information on protesters who damaged statues and monuments. The committee has received internal documents and is preparing to interview witnesses on the agency’s deployment of tactical agents to Portland, Ore.
Representative Adam B. Schiff, the chairman of the committee, said in a letter on Friday that it had expanded its investigation to include the “improper politicization of intelligence and political interference.” The Republican-led intelligence committee in the Senate notified the department on Thursday that it, too, would investigate on a bipartisan basis claims made by Mr. Murphy.
Mr. Murphy is expected to testify on Sept. 21 in a closed-door session with the committee. The House Homeland Security Committee also issued a subpoena to Mr. Wolf to testify in a public hearing on Sept. 17 after he refused to commit to doing so by citing his pending nomination.
He has gone from accused to accuser in a matter of weeks. Previous witnesses against the Trump administration, such as Alexander S. Vindman and Marie L. Yovanovitch, have been painted by critics of the president in golden hues. Mr. Murphy is more complicated: Last month, Mr. Schiff said he was concerned Mr. Murphy had misled Congress over the office’s intelligence gathering methods during the unrest in Portland.
Mr. Murphy, a conservative Republican who supported Mr. Trump in 2016, saw the senior intelligence position at homeland security as a logical next step for his counterterrorism career, former officials who worked with him said. His work at the F.B.I. earned him the nickname T-1000, after the almost indestructible, relentless android in the movie “Terminator 2.”
But his brusque style and penchant for going alone over repeated warnings from superiors to hew more closely to the rules ultimately stalled his career at the F.B.I. before he could land a plum assignment running a field office, a former senior law enforcement official said.
In interviews, former colleagues saw him as a “freelancer” who was determined to see investigations to the end, even if it meant ignoring unwritten rules of an institution. That reputation led some in F.B.I. leadership and the Justice Department to sour on him, according to interviews with nine former colleagues who requested anonymity to speak candidly about the whistle-blower and the homeland security intelligence office.
Mr. Murphy’s commitment to collaborating with state and local law governments also made the Office of Intelligence and Analysis at the Homeland Security Department attractive.
The department’s intelligence office has struggled to distinguish itself from other intelligence agencies as a source for information since it was created in 2007, five years after the Homeland Security Act of 2002 conjured its legal existence.
The analysts in the intelligence office comb through publicly available information and coordinate with other federal agencies to draft unclassified intelligence briefings for state officials.
But as the F.B.I. has built up its own partnerships with local police departments and placed bureau agents in information-sharing “fusion centers,” some law enforcement officials have questioned the quality of the homeland security intelligence office’s reports.
“It’s one thing to own the investigation and report out the investigation and develop an intel product as a result of that,” Mr. Sleeper said. “It’s another thing to report out on someone else’s investigation,” which homeland security does.
That reliance on other people’s information has created problems. When the homeland security intelligence office relied heavily on international trade data to claim that Chinese central government officials hid the severity of the coronavirus in early January in order to hoard medical gear, analysts in the broader American intelligence community objected and issued a report saying officials in Beijing were kept in the dark for weeks about the virus’s devastating potential.
John Cohen, who led the homeland security intelligence agency in the Obama administration, said the agency has always faced questions of, “What does it bring to the table? What can it do differently than other agencies?”
Mr. Cohen said the office was most effective when it used the resources of the sprawling Homeland Security Department, such as Customs and Border Protection and the Transportation Security Administration, to produce detailed analyses of security vulnerabilities in the department’s purview, such as the nation’s transportation systems.
Some of the agency’s hundreds of analysts and intelligence officers also sift through travel and immigration data to help vet those coming to the United States.
Mr. Murphy charged in his complaint that Kenneth T. Cuccinelli, the acting deputy secretary of the department, directed him to fire analysts who compiled reports showing high levels of corruption, poverty and violence in Central American countries. Such information could undermine Mr. Trump’s goal of blocking migrants from obtaining asylum.
Before his demotion, Mr. Murphy was determined to carve a distinct lane for the agency, Mr. Sleeper said.
“He went into it with eyes wide open,” Mr. Sleeper said.
Mr. Murphy emphasized to another former colleague the need to distance the office from what he viewed as the politicization that had enthralled the Homeland Security Department.
Mr. Murphy, who earned a master’s degree in Islamic Studies from Columbia University, served in the Marines from 1994 to 1998 and was decorated for combat in Iraq after deploying there in 2004. In 2007, Esquire magazine profiled him under the headline, “Brian Murphy v. the Bad Guys.”
The article recounted Mr. Murphy’s role in a terrorism financing investigation in 2003 involving a Yemeni cleric. “One extraordinary agent pursued and won a terrorism case without changing the standards of American justice,” the article proclaimed.
A federal jury in New York found the cleric and an aide guilty of funneling money to terrorist groups, helping propel Mr. Murphy’s career.
But that triumph soured in dramatic fashion. After an appeals court overturned the convictions and ordered a new trial, the cleric and his aide cut a deal with prosecutors and were eventually freed. Then the informer whom Mr. Murphy used during the investigation set himself on fire in front of the White House, claiming federal agents had treated him poorly.
Mr. Murphy nonetheless continued his ascent, becoming a senior agent at F.B.I. headquarters overseeing the program to counter violent extremism.
At times, he could grate on people with his certitude. He pushed a plan to have community leaders, such as coaches and social workers who work with young people vulnerable to radicalization, sign memorandums agreeing to share what they learned with the F.B.I. Some agents agreed it was a good alternative to possible prosecution, but it also would have allowed the F.B.I. to essentially deputize social workers to track people who had committed no crimes. Officials worried the initiative would fuel suspicions in Muslim communities that the bureau was using outreach to spy on them.
A similar effort by Mr. Murphy in Chicago had troubled lawyers at the Justice Department, former officials said.
“He wasn’t always the most politically correct,” Mr. Cohen said.
Nicholas Fandos and Eric Schmitt contributed reporting. Kitty Bennett contributed research.