Shortly after the World Health Organization declared the Ebola outbreak in Africa a public health emergency, a reporter asked Health Secretary Robert F. Kennedy Jr. if he was worried about the virus. Six Americans had already been exposed. His response was brief: “Yeah, we’re working on it.”

In the nearly three weeks since, as the Centers for Disease Control and Prevention imposed travel restrictions to keep the virus from coming to the United States, Mr. Kennedy has made no public comments about the spreading outbreak. He has received very few briefings about the virus from C.D.C. scientists, although he speaks daily to the acting director, according to people familiar with his response.

Mr. Kennedy’s approach to the crisis reflects his broader management of the Department of Health and Human Services, which affects the health of 340 million Americans and provides health care to 40 percent of the population through Medicare and Medicaid.

Mr. Kennedy has shown little interest in managing the details of work in his department, according to multiple colleagues. Instead, they say, he is single-mindedly focused on his top priorities, including food recommendations and pesticide exposures, and hunting for evidence to support his long-held beliefs that vaccines are harmful.

Deeply mistrustful of career civil officials, the secretary has surrounded himself with a close circle of handpicked advisers and stacked agencies with political appointees aligned with his views. While major posts have sat vacant and a wave of veteran health experts and scientists have departed, Mr. Kennedy has remained isolated from much of the department’s top staff.

He rarely engages with members of Congress, colleagues said, unless he is asked to testify. He has made just one known visit to the C.D.C., after a gunman opened fire on its headquarters and killed a police officer last August.

This examination of Mr. Kennedy’s leadership style is based on the accounts of a dozen people who have had direct contact with him as secretary, as well as other health department employees, all of whom spoke on the condition of anonymity to avoid retribution.

Mr. Kennedy and the department did not directly address questions about his leadership style.

The secretary’s detachment from much of the work of the agency, along with the administration’s deep staff cuts and his attacks on career staff, have driven down morale, they say. It’s a dynamic that could threaten the department’s ability to protect Americans in a crisis, according to public health experts and former secretaries.

Critics say one of the most urgent problems is Mr. Kennedy’s failure to act more swiftly to address a leadership vacuum. There is no surgeon general. Around half of the 27 institutes and centers at N.I.H. are run by acting directors. The acting chief of the National Institute for Allergy and Infectious Diseases was recently fired, as was the nation’s top drug regulator.

The leader of the Food and Drug Administration quit last month under pressure over tobacco policy. Mr. Kennedy fired the C.D.C. director last August; it is now run on an acting basis by Dr. Jay Bhattacharya, who already has another huge job as director of the National Institutes of Health.

“You would never accept a major corporation operating this way,” said Michael T. Osterholm, the director of the University of Minnesota Center for Infectious Disease Research and Policy, who has advised health secretaries of both parties.

“If the C.E.O. lacked deep expertise in the company’s business and the leaders of its most important divisions were missing, investors would revolt,” Dr. Osterholm said. “Here, the stakes are much higher. The mission is protecting the health and safety of the American people, and we’re confronting serious disease threats without permanent leadership in some of our most important public health agencies.”

To address the management gaps, the White House and Mr. Kennedy initiated a shake-up in February, elevating Christopher Klomp, a department official and former health care executive, to serve as the secretary’s chief counselor and smooth out operations. In a statement, Courtney Spencer, who left the Labor Department two weeks ago to become Mr. Kennedy’s top spokeswoman, said the health department was “aggressively recruiting top talent to fill every remaining vacancy,” adding, “Nothing has slowed our ability to execute.”

Mr. Kennedy’s allies say that while his management style may be different from that of his predecessors, he is leading in other ways by taking stands on matters of importance to Americans, including healthy eating and tackling chronic disease.

“You do not come to Washington to challenge powerful interests, disrupt decades of business as usual, and demand accountability to make friends,” Dr. Mehmet Oz, the director of the Centers for Medicare and Medicaid Services and a close ally of Mr. Kennedy’s, said in a statement provided by the health department. “You do it to deliver results.”

Other advisers say Mr. Kennedy is also running into the realities of Washington, including a Congress that has refused to confirm some of President Trump’s nominees.

“Very predictably, you get into governing, you get into a toxic political environment, and a situation where there’s trillions of dollars of interest and you have the burden of having to do policy,” Calley Means, a close adviser to Mr. Kennedy, said at a recent forum hosted by Harvard University. “Nobody executes perfectly.”

A Remote Presence

Mr. Kennedy keeps a low profile at the health department’s headquarters, a hulking building that faces the National Mall near the U.S. Capitol.

When he is in town, he exercises at his gym before work, then usually arrives at about 10 a.m. and leaves by 4 p.m., his colleagues say. He spends much of his day in closed-door meetings, according to those who work with him, and has little direct engagement with his staff.

Every Tuesday at 10:30 a.m., the chiefs of the department’s 13 operating divisions gather in the secretary’s suite to update leadership on their activities. At the outset of his tenure, Mr. Kennedy was rarely there, either virtually or in person, according to three people familiar with his schedule. Since Mr. Klomp’s elevation, he now shows up once a month. But when he does attend, he often appears disengaged and spends the time scrolling on his phone, according to people in attendance. Several described him as “checked out.”

Once, when he arrived to the meeting 15 minutes late, Mr. Kennedy offered a self-deprecating apology, according to one person in the room: “Thank you for putting up with my dysfunctional self.”

Health department officials did not respond to a request for comment about the meeting or Mr. Kennedy’s remark.

His disinterest in matters that are not high on his priority list has meant that he has not engaged at critical moments, colleagues said.

When measles killed two children in Texas early last year, Dr. Demetre Daskalakis, who led the response but has since left the agency, asked repeatedly to brief Mr. Kennedy but was rebuffed, he said.

Susan Monarez, who briefly served as Mr. Kennedy’s C.D.C. director before she was fired, had little direct interaction with the health secretary until she ran afoul of him on vaccine policy. She later told senators that during a series of tense meetings with the secretary, she was “directed to only work with the political appointees that he had put in place at C.D.C., and not to speak or work with the career scientists.”

In the current Ebola crisis, Mr. Kennedy has left the department’s response to Dr. Bhattacharya, a health economist with no prior experience in public health even though he is leading the C.D.C. Dr. Bhattacharya, who also led the response to a recent outbreak of hantavirus, wrote an opinion essay published in The Wall Street Journal on Wednesday saying that while the “risk to the American public remains low, Ebola is dangerous.”

A White House spokesman, Kush Desai, said the agency’s “rapid and comprehensive response” to the Ebola outbreak proved that “under Secretary Kennedy’s leadership, H.H.S. continues to safeguard the health and wellness of the American people.”

Ms. Spencer, the H.H.S. spokeswoman, said the health department had “executed an immediate and coordinated response” under Mr. Kennedy’s leadership.

But key vacancies inside the health department have made the response more challenging, people familiar with situation said.

The Administration for Strategic Preparedness and Response, responsible for pandemic preparedness and for standing up field hospitals and quarantine facilities in Kenya, is currently run on an acting basis by John Knox, a former Los Angeles firefighter who founded the group Firefighters4Freedom during the pandemic to fight vaccine mandates.

As the outbreak has spread, Secretary of State Marco Rubio offered a tacit rebuke of Mr. Kennedy’s move last year to withhold funding from an international vaccine alliance, suggesting the State Department was taking back management of the U.S. relationship with the alliance.

“We are going to re-engage,” Mr. Rubio told lawmakers last week. “We need to drive this to an outcome.”

A Daunting Portfolio

Under any circumstances, the Department of Health and Human Services is difficult to run. It has 13 operating divisions covering a vast array of issues, such as child welfare and pandemic preparedness. Past secretaries from both political parties say there are three main ingredients for success: understanding the work of the divisions, strong crisis communication and muscular coordination with state, local and international health leaders.

Tommy G. Thompson, who as health secretary to President George W. Bush faced complaints about his management of the 2001 anthrax crisis, spent a week at each one of the operating divisions at the outset of his tenure, and made frequent trips to Capitol Hill to advocate for the department. In an interview last year, he said he “would strongly suggest” Mr. Kennedy do the same.

“The department is so vast and so complex,” Mr. Thompson said, “and you have to be prepared.”

Kathleen Sebelius, a former Kansas governor who resigned as President Barack Obama’s health secretary after the flawed rollout of the healthcare.gov website, said she met with the division chiefs regularly, likening them to her cabinet.

“My goal was to really be informed by the scientists, to make sure that N.I.H. was at the table, that F.D.A. was at the table, that our global health people were at the table,” Ms. Sebelius said in an interview, adding, “I was really schooled by the people who had been there before and who knew what the hell they were doing.”

Mr. Kennedy, by contrast, has delegated broad authority to Stefanie Spear, a longtime adviser who has been with him since his days as an environmental lawyer and functions as his protector and defender, according to people who know them.

Ms. Spear runs meetings for the secretary, accompanies him on official trips and keeps a list of the secretary’s policy projects on a private spreadsheet to which his policy team has no access; there are more than 50 items on the list, one person who has seen it said.

All of the requests for the secretary’s decisions and meetings go through Ms. Spear. When Mr. Kennedy is asked a question, his frequent response is “just run that by Stefanie.”

Colleagues say that her tight control has slowed down department operations.

After Mr. Kennedy promised Congress that the F.D.A. would investigate the safety of the abortion pill mifepristone, the agency proposed updating a set of sophisticated databases of electronic records it needed for the research. But the project was delayed for months by Mr. Kennedy’s office, according to two people with detailed knowledge.

When a gunman opened fire on the C.D.C. last August, Mr. Kennedy was fishing with Native American leaders in Alaska. Health department officials wanted to get a statement out to the news media. But it was held up for hours, several said, while Ms. Spear sought approval from the White House.

Frustration with Ms. Spear, who served as Mr. Kennedy’s communications director during his campaign and oversees his public comments, has fueled some key departures.

Mr. Kennedy is on his third top spokesman; the first two quit in frustration, according to people familiar with their decisions. The secretary has also run through two chiefs of staff; he fired the first one, and the second was pushed aside in favor of Mr. Klomp.

In a statement, Mr. Kennedy praised Mr. Klomp and Ms. Spear as “two of the most effective leaders in government.” He said Mr. Klomp had ”been instrumental in driving operational excellence, strengthening accountability, and ensuring H.H.S. delivers results for the American people,” and that Ms. Spear “keeps our team focused on results and ensures the president’s and my priorities get across the finish line.”

Mr. Klomp has moved quickly in the search for a new C.D.C. director, with a nominee now awaiting Senate confirmation, as well as for other top leaders for the agency. He also brought in a new team of policy advisers to the secretary and instituted daily meetings between Mr. Kennedy and the leaders of the “Big Four” agencies: F.D.A., C.D.C., N.I.H. and the Centers for Medicare and Medicaid Services, according to three people familiar with the department’s operations.

He has also sought to address low morale by starting a regular newsletter in which Mr. Kennedy addresses employees as “the dedicated professionals of H.H.S.”

The secretary, however, has been out of the loop on some key decisions. When Dr. Tracy Beth Hoeg, the F.D.A.’s top drug regulator, was fired by F.D.A. leaders in May, the secretary did not learn of it until after it happened, according to three people familiar with the events.

There is no question that Mr. Kennedy is changing the national conversation around health in America, especially healthy eating. While his vaccine agenda has so far been stymied by court decisions, he has scored “wins,” as he likes to call them, notably by flipping the food pyramid, persuading medical schools to revamp nutrition education and convincing some food makers to abandon artificial dyes.

He travels often and makes aggressive use of his platform to promote his priorities, including on social media and “The Secretary Kennedy Podcast,” which began in April. Last week, he made stops in Wisconsin to spotlight the work of dairy farmers and faith-based groups working in addiction recovery, and New Hampshire to announce an effort to combat Lyme disease.

Colleagues say he also makes visits to Scottsdale, Ariz., where his son and daughter-in-law live, and Florida, where he stays at the Palm Beach mansion owned by Dr. Oz.

After Memorial Day, the public got a glimpse of him there. Mr. Kennedy posted video of himself, in a suit and tie, capturing two black racer snakes on Dr. Oz’s patio. One of them bit him.

Apoorva Mandavilli contributed reporting.