The day began with tweets from the president falsely claiming that the number of deaths attributable to Maria had been inflated by Democrats to “make me look as bad as possible.” Long said that despite the distractions, he and his agency are “100 percent” focused on the hurricane. “That’s exactly where our attention needs to be from the standpoint of the life safety mission,” he said at a media briefing.

Current and former FEMA officials said it was alarming to see the nation’s top officials engaged in political skirmishes as Florence was due to make landfall with the potential to displace millions of people and devastate swaths of the Southeast. The news, first reported by Politico, was initially disclosed by current and former Trump administration officials, fueling the sense of frustration felt by those with ties to the agency.

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“The fact that someone within the administration is taking shots at FEMA in the middle of a hurricane is insane,” said a former top FEMA official, who, like others, spoke on the condition of anonymity to discuss a sensitive personnel matter. “Lives are at stake. People are working around the clock to get resources and assets in place. . . . Why would you do that?”

The former FEMA official said that although the investigation was made public on Thursday, its existence has been known for months, making its disclosure in the middle of the storm untimely and bizarre.

The inspector general at the Department of Homeland Security is investigating Long for allegedly using a government vehicle to travel between Washington, D.C., and his home in Hickory, N.C., where wife and two young children live, according to a DHS official familiar with the situation.

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At a media briefing Thursday morning, Long denied doing anything improper, saying, “I would never intentionally run a program incorrectly. . . . Doing something unethical is not part of my DNA and is not part of my track record my entire career.”

Long said, “We’ll continue to fully cooperate with any investigation that goes on. And own up to any mistakes and push forward, and keep going, keep moving on. But here’s the thing, regardless of an article, right now I am 100 percent focused” on Hurricane Florence.

A DHS official who knows him said Long is “crestfallen” by the investigation and that Long refused to step down last week when Nielsen asked him to resign. The official said Nielsen has been trying to push him out for months, “hounding” him about not being in the office more because he goes back to North Carolina on weekends and that Long believes Nielsen wants to replace him with someone loyal to her.

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“This is a guy going to church in Hickory, North Carolina,” the official said. “He’s a Boy Scout. This is a guy with a young family trying to get home to see his kid’s baseball games on the weekends. This is not a Scott Pruitt-type situation.”

Pruitt, who led the Environmental Protection Agency, resigned in July amid scrutiny of his spending and travel.

Another DHS official who works with Nielsen denied that she asked Long to step down or has wanted to push him out. But several current and former officials at DHS and FEMA said the squabble has thrust a leadership struggle into the public spotlight.

DHS spokesman Tyler Q. Houlton referred questions to the agency’s Office of the Inspector General, saying: “At this time, we are fully focused on preparing for, responding to, and recovering from Hurricane Florence and the storms in the Pacific. The Secretary is confident in the leadership at FEMA and their proven disaster management ability.”

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A spokesman for the inspector general’s office did not immediately respond to a request for comment.

Current and former FEMA officials said one reason Long likely traveled in a government SUV, driven by a government driver, on trips home to North Carolina was the specialized communications onboard that allow him to maintain contact with his agency and the White House — an important consideration for the nation’s top disaster official. Other administrators said they have also used such vehicles on trips in the past, although less frequently.

R. David Paulison, former FEMA administrator under President George W. Bush, said he rarely flew home to Florida while in the job because its relentless pace kept him in Washington. “But I missed meetings with governors a few times because I was flying commercial so the White House put me on private jets in a few emergencies,” he said. “The communications gear has also changed a great deal since then.”

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W. Craig Fugate, President Obama’s FEMA administrator, said he mostly drove his personal vehicle or flew at his own expense when visiting his home in Gainesville, Fla., but there were also six or seven times during his eight-year tenure when FEMA staff deployed a government SUV, mostly to keep him in secure communication with Washington.

Long’s nomination was widely praised by other emergency officials because of his previous experience. He was emergency management director for the state of Alabama and, before that, a FEMA regional hurricane program manager and FEMA hurricane and evacuation liaison team leader.

“He’s well liked in the agency, because he took a lot of arrows for FEMA. When people wanted to criticize what happened with Harvey or Maria, he was the guy who showed up on TV to take those arrows,” said one former top FEMA official.

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After an internal investigation of alleged sexual misconduct by FEMA’s former human relations chief, Long mounted a campaign against sexual harassment, including the creation of several committees to change the agency’s culture, which several current FEMA staffers said gained him credibility and admiration among the rank and file.

In his tweets Thursday, Trump falsely claimed that Democrats had conspired with researchers at George Washington University to hike the estimated death toll from Maria. The researchers pushed back, saying they were under no political pressure and used scientific rigor to reach their estimate of 2,975 “excess deaths” from Maria and its aftermath.

Trump has also said in recent days that the FEMA effort in Puerto Rico was “an incredible, unsung success,” but FEMA’s own after-action report and a separate Government Accountability Office report have painted a bleaker picture.

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The FEMA internal report acknowledged that the agency had never planned for a hurricane as powerful and devastating as Maria, or anticipated two hurricanes hitting back to back, and it revealed that an emergency warehouse in Puerto Rico had been largely emptied of supplies such as cots, tarps and water, which had been dispatched to the U.S. Virgin Islands to deal with impacts from Hurricane Irma.

The GAO report described FEMA as “overwhelmed” by Maria and noted high numbers of FEMA workers who were unqualified to do their jobs and in some cases not physically fit to handle the harsh working environment.

Emergency officials said staffers at FEMA are trying to ignore the controversies.

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“You have people who have been working 16-hour days, seven days a week. And you have a season ahead that’s going to mean working 40, 50 days in a row without break,” said one former FEMA official. “The people at this agency are at their best when responding to disasters. So luckily, morale isn’t really a problem at a time like this. Folks are just focusing on doing everything they can to save people’s lives.”