WASHINGTON — President Biden, who came into office vowing to “reinvigorate our national science and technology strategy,” is now facing a leadership vacuum that may threaten his ambitious research agenda, which stretches well beyond fighting the coronavirus pandemic.

Both the Food and Drug Administration and the National Institutes of Health lack permanent leaders. Mr. Biden’s health secretary, Xavier Becerra, has been criticized for his low profile. And on Monday, his science adviser, Dr. Eric S. Lander — the first such adviser to serve in the cabinet — resigned after acknowledging that he had bullied his colleagues.

Dr. Lander’s departure leaves a particularly big hole. He was in charge of the “cancer moonshot,” an initiative to cut death rates from cancer in half over the next 25 years, and was behind a new pandemic preparedness plan that the White House has likened to the Apollo mission.

Dr. Lander was also a driving force behind Mr. Biden’s proposal to create a new agency to propel innovation in medical research. Modeled after the Defense Advanced Research Projects Agency, the proposed agency, known as ARPA-H, was the subject of a House committee hearing on Tuesday. Dr. Lander, who was supposed to be the key witness, was not there.

“This was an administration that really committed to the primacy of science for the pandemic and also aspirations for well beyond the pandemic,” said Dr. Eric Topol, the founder and director of the Scripps Research Translational Institute. “And what it has been on is a self-inflicting harm mission.”

Administration officials say the work will carry on. Kevin Munoz, a White House spokesman, said the administration has “exceptional leadership” at the Department of Health and Human Services, and “strong acting leadership” at the F.D.A. and the health institutes.

The F.D.A. is being run by an acting commissioner, Dr. Janet Woodcock, and Dr. Lawrence Tabak is the acting director of the N.I.H. after its longtime leader, Dr. Francis S. Collins, stepped down late last year. Both Dr. Woodcock and Dr. Tabak are longtime officials at their respective agencies, regarded as steady hands.

But Sudip Parikh, the chief executive of the American Association for the Advancement of Science, said he was deeply concerned that, without permanent leaders, it would be difficult for federal agencies to carry out Mr. Biden’s agenda with imagination and vision.

In addition to considering whether to create and fund ARPA-H, the House and the Senate are working to reconcile their versions of legislation authorizing an increase in funding for the National Science Foundation, which would expand research in a range of science and technology fields, like quantum computing and artificial intelligence.

“I am excited about what we have accomplished so far, but I am really worried about this next set of steps,” Dr. Parikh said. “We are on the cusp of some of the biggest changes to the way we do science in this country in 74 years, so we want Senate-confirmed scientific leaders that can put forth a vision.”

Ellen Sigal, the chairwoman and founder of Friends of Cancer Research, an advocacy group in Washington, shares that concern.

“They promptly need to have an F.D.A. commissioner confirmed, they have to have an announcement on who will direct the N.I.H. and then they are going to have to replace Dr. Lander and figure out who has the stature to bring these various initiatives together,” she said.

After the administration of former President Donald J. Trump, who routinely spread misinformation about the coronavirus, scientists were thrilled and relieved when Mr. Biden was elected.

“Our long national nightmare is over,” R. Alta Charo, professor emerita of law and bioethics at the University of Wisconsin, told Scientific American at the time.

In an interview on Thursday, Ms. Charo said Mr. Biden had fulfilled his pledge of respecting scientific integrity, and his response to the pandemic, while not perfect, had been a big improvement. Still, she said, “I think it’s appalling that we have such a vacuum of leadership.”

Others have been less charitable. Holden Thorp, a former chancellor of the University of North Carolina at Chapel Hill who is now the editor in chief of Science, published an editorial on Tuesday calling Dr. Lander’s departure “the latest disappointment from an administration that has been struggling to guide the nation with sound science and science leadership.”

Some critics of the administration say Mr. Biden brought some of the problems on himself with the people he chose to put in various leadership positions.

He waited until nearly a year into his presidency to name Dr. Robert Califf, a former deputy F.D.A. commissioner, as his nominee for the top job, knowing all the while that Dr. Califf’s ties to the drug industry would generate opposition among some Democrats. Dr. Califf now faces a steep climb to confirmation, with key Democrats withholding support over opioid policies and his industry ties, while anti-abortion groups are pressuring Republicans to vote against him.

Mr. Biden picked Dr. Lander — a leading geneticist, to run the Office of Science and Technology Policy despite serious questions about his behavior in the workplace. Dr. Lander had previously been accused of being insensitive to women and people of color. During his Senate confirmation hearing, he acknowledged downplaying the contributions of two female scientists, who last year won a Nobel Prize for their work on gene-editing technology.

Mr. Becerra — a former California attorney general whose passion is improving access to health care — also seemed an odd choice to run the Department of Health and Human Services during a pandemic, when public health expertise was needed. At his confirmation hearing, he was grilled by Republicans who complained he had no medical background.

Mr. Becerra’s defenders say Mr. Biden put him in a difficult spot; by centralizing the pandemic response in the White House and putting doctors like Anthony S. Fauci before the television cameras, the health secretary was pushed into the background. And at the time Mr. Becerra was chosen and confirmed, the Biden administration had hoped its vaccination campaign would bring a swift end to the pandemic.

But several current and former administration officials have said that while Mr. Becerra is well liked, he has not flexed his muscles to resolve conflicts between the agencies under his purview, including the F.D.A. and the Centers for Disease Control and Prevention. That has created a structural problem with the pandemic response: Difficult public health decisions are essentially hammered out by a handful of senior health officials, none of whom is in charge.

“N.I.H., C.D.C. and F.D.A. playing nicely together is just not a natural act,” said Dr. Nicole Lurie, a top health official under former President Barack Obama. “The sibling rivalry is intense and there needs to be some strong presence to help coordinate and surface the gaps.”

In recent days, the administration has sought to elevate Mr. Becerra’s profile. Jeffrey D. Zients, the White House coronavirus response coordinator, took pains at a briefing on Wednesday to note that his team was coordinating with Mr. Becerra. Also on Wednesday, Mr. Becerra traveled with Jill Biden, the first lady, to Minneapolis to talk about child care. On Thursday, he went with the president to Culpeper, Va., to talk about lowering drug costs.

In an interview in November, Mr. Becerra said he did not need to be in the spotlight to succeed in his job. He referred to his time as a member of Congress, when he was in Democratic leadership, including leading the House Democratic Caucus.

“I was never the most vocal — tell me if you ever recall me sort of being the guy that always was in front of the camera,” he said. “I do believe there is something about speaking softly but carrying a big stick.”