President Biden on Thursday announced he would nominate Rick Spinrad, a professor of oceanography at Oregon State University, to head the National Oceanic and Atmospheric Administration, the country’s premier climate science agency.

The announcement potentially marks a new chapter for NOAA, which was at times a source of tension for former President Donald J. Trump, who publicly sparred with the agency’s scientists and was unable to get any of his nominees to lead it confirmed by the Senate. NOAA has been without a Senate-confirmed leader for the longest period since it was created in 1970.

In 2019, Mick Mulvaney, who was Mr. Trump’s acting White House chief of staff at the time, pushed NOAA to disavow statements by its weather forecasters that contradicted what the president had said about the path of Hurricane Dorian. Last year, the administration removed NOAA’s chief scientist from his role and installed people who questioned the science of climate change in senior roles at the agency.

Dr. Spinrad is a former chief scientist at NOAA, where he also led the agency’s research office and the National Ocean Service. The timing of Mr. Biden’s announcement was notable — on Earth Day amid a two-day climate summit in which he committed the United States to cutting emissions by half by the end of the decade.

The selection of Dr. Spinrad drew quick praise from the scientific policy community Thursday evening.

“We commend the Biden administration for continuing to nominate credible and well-qualified candidates who understand the urgency of the climate crisis,” Sally Yozell, the director of the environmental security program at the Stimson Center, a Washington think tank, said in a statement.

Rear Adm. Jonathan White, the president and chief executive of the Consortium for Ocean Leadership, called Dr. Spinrad “an excellent choice for this important role.”

WASHINGTON — Federal regulators have found serious flaws at the Baltimore plant that had to throw out up to 15 million possibly contaminated doses of Johnson & Johnson’s coronavirus vaccine — casting doubt on further production in the United States of a vaccine that the government once viewed as essential in fighting the pandemic.

The regulators for the Food and Drug Administration said that the company manufacturing the vaccine, Emergent BioSolutions, may have contaminated additional doses at the plant. They said the company failed to fully investigate the contamination, while also finding fault with the plant’s disinfection practices, size and design, handling of raw materials and training of workers.

“There is no assurance that other batches have not been subject to cross-contamination,” the F.D.A.’s 12-page report states.

The report amounted to a harsh rebuke of Emergent, which had long played down setbacks at the factory, and added to problems for Johnson & Johnson, whose vaccine had been seen as a game changer because it requires only one shot, can be produced in mass volume and is easily stored.

Production is now on pause in the United States, and all vaccines manufactured at the plant have been quarantined. Johnson & Johnson has fallen well behind on its promises to deliver tens of millions of doses to the federal government, in part because concerns about an extremely rare but dangerous blood-clotting disorder led federal officials last week to temporarily halt distribution.

The F.D.A. findings, based on an inspection that ended on Tuesday, underscore questions raised in reports by The New York Times about why Emergent did not fix problems earlier and why federal officials who oversee its lucrative contracts did not demand better performance.

A series of confidential audits last year, obtained by The Times, warned about risks of viral and bacterial contamination and a lack of proper sanitation at the Baltimore plant. Separately, The Times reported, a top federal manufacturing expert cautioned last June that Emergent would have to be “monitored closely.”

Some health officials were taken aback by the F.D.A.’s conclusions.

“I’m shocked — I can’t put it any other way,” said Dr. José R. Romero, chairman of a panel advising the Centers for Disease Control and Prevention that later this week will recommend how to handle the Johnson & Johnson vaccine. “Inappropriate disinfection, the prevention of contamination — those are significant and serious violations.”

In statements on Wednesday, the F.D.A., Emergent and Johnson & Johnson all said they were working to resolve the problems at the factory. There was no indication of how long that would take.

Emergent said that “while we are never satisfied to see shortcomings in our manufacturing facilities or process, they are correctable and we will take swift action to remedy them.”

The F.D.A. has not yet certified the plant, located in Baltimore’s Bayview neighborhood, and no doses made there have been gone to the public. All the Johnson & Johnson shots that have been administered in the United States have come from overseas.

In a statement, Dr. Janet Woodcock, the F.D.A.’s acting commissioner, and Dr. Peter Marks, its top vaccine regulator, said: “We will not allow the release of any product until we feel confident that it meets our expectations for quality.”

Emergent is a longtime government contractor that has spent much of the last two decades cornering a market in federal biodefense spending.

Though the government gave Emergent a $163 million contract in 2012 to ready the Baltimore plant for mass production in a pandemic, the site remained largely untested, and the company did not meet a requirement for demonstrating its rapid-response capabilities, according to former health officials and contracting documents.

Nonetheless, the government went on to award Emergent a $628 million contract last June, most of it to reserve manufacturing space at the plant, and arranged for the company to produce the Johnson & Johnson shot and a separate vaccine developed by AstraZeneca.

Now, Emergent’s dealings with the government are under increasing scrutiny. On Tuesday, the House Select Subcommittee on the Coronavirus Crisis and the House Committee on Oversight and Government Reform announced an investigation into the company’s Covid-19 vaccine contract, as well as its longstanding hold on an outsize portion of the budget for the nation’s emergency medical reserve, the Strategic National Stockpile.

A Times investigation found that purchases of the company’s anthrax vaccine had accounted for almost half the reserve’s entire annual budget for much of the last decade — leaving less money for critical supplies like masks that were scarce last year.

The Bayview plant was supposed to produce the bulk of the Johnson & Johnson vaccine, which received federal authorization for emergency use this year but only for doses made in the Netherlands. AstraZeneca’s vaccine is not yet allowed in the United States, regardless of where it is manufactured.

The F.D.A. inspection began after routine checks showed that Emergent workers had contaminated at least part of a batch of 13 million to 15 million doses of the Johnson & Johnson vaccine with the harmless virus that is used to make the AstraZeneca shot. The regulators found that Emergent failed to thoroughly investigate that incident and performed only routine cleaning afterward. One previous audit of Bayview for a pharmaceutical customer found that Emergent glossed over deviations from manufacturing standards without conducting thorough reviews.

The inspectors, who examined security footage as part of their review, found that Emergent failed to consider whether one or more workers might have been the source of the contamination. Workers are supposed to change gowns and bootees and shower before crossing between the different manufacturing zones for Johnson & Johnson and AstraZeneca.

But the regulators said that rule appeared to be routinely violated. In one 10-day period in February, for instance, 13 employees moved from one zone to another on the same day, but only one documented having showered, they said. The inspectors also said Emergent failed to consider whether using common storage containers for raw materials might have caused the contamination. Emergent’s own internal audit last July said the flow of workers and materials through the plant was not adequately controlled “to prevent mix-ups or contamination.”

Federal officials have already insisted on a major change they say should significantly limit risks. This month, they ordered Emergent to stop making the AstraZeneca shot at the plant, and they are now trying to help AstraZeneca find a new manufacturing site.

In another finding, the F.D.A. regulators wrote that the Bayview building “is not maintained in a clean and sanitary condition.” Nor is it “of suitable size, design and location to facilitate cleaning, maintenance and proper operations,” they said.

They cited peeling paint, damaged walls, improperly trained employees, overcrowded equipment and poor waste management, an issue they said could lead to contamination of the warehouse where raw materials are stored.

The findings were released two days before the expert advisory panel of the C.D.C. was scheduled to vote on whether to extend, lift or modify the Johnson & Johnson suspension. Officials recommended the pause in order to investigate eight cases of a rare clotting disorder in vaccine recipients, one of them fatal.

Johnson & Johnson resumed its rollout in Europe this week after regulators investigated similar concerns. They recommended that a warning about the blood clots should be attached to the vaccine’s label, but said the benefits outweighed the risks.

The inspection report comes as a group of shareholders are suing Emergent, alleging that executives misled investors about the company’s ability to manufacture Covid-19 vaccines in Baltimore.

After announcements last year of deals with the federal government, Johnson & Johnson and AstraZeneca totaling $1.5 billion, Emergent’s share price climbed. Throughout 2020, its founder and chairman, Fuad El-Hibri, cashed in shares and options worth over $42 million, and the company’s chief executive, Robert Kramer, was recently awarded a $1.2 million cash bonus.

The lawsuit alleges that the stock price was artificially inflated because executives failed to disclose significant quality-control problems at the facility. Emergent’s stock has tumbled in recent weeks.

Shortly after the Trump administration’s Operation Warp Speed decided to award Emergent the $628 million contract, Carlo de Notaristefani, a manufacturing expert who has overseen vaccine production for the federal government since last May, warned the company “will have to strengthen” its quality controls, requiring “significant resources and commitment. ”

Dr. Robert Kadlec, the former Trump administration official who oversaw the awarding of the contract, said in an interview on Tuesday that officials “recognized that there were going to be inherent risks” but said the government intended to “try to mitigate those risks throughout.”

Dr. Romero, the C.D.C. advisory panel leader who is also the Arkansas health secretary, was concerned that the plant’s problems could discourage people from getting vaccinated, even though doses from there have not reached the public. Andy Slavitt, a top health adviser to President Biden, told reporters that the audit showed “a process that is working as it should.”

Johnson & Johnson said it had already increased oversight of Emergent, and that it would “ensure that all of F.D.A.’s observations are addressed promptly and comprehensively.”

The pharmaceutical company is expected to nearly double its supervisors at the Bayview plant, to perhaps a dozen, though Emergent will continue providing a work force of about 600 employees.