An Operation Warp Speed report last June flagged staffing and quality control concerns at Emergent BioSolutions’ factory in Baltimore. The troubled plant recently had to throw out up to 15 million doses.WASHINGTON — A top federal pandemic official warned last June that Emergent BioSolutions, the government contractor that last month threw out millions of doses of Covid-19 vaccines because of contamination, lacked enough trained staff and had a record of problems with quality control.A copy of the official’s assessment, obtained by The New York Times, cited “key risks” in relying on Emergent to handle the production of vaccines developed by both Johnson & Johnson and AstraZeneca at Emergent’s Bayview plant in Baltimore.The assessment, which has not been released publicly, was based in part on a visit to the plant just days after the government awarded Emergent a contract worth up to $628 million, mostly to prepare its factories to make coronavirus vaccines as part of Operation Warp Speed.Addressing the problems “will require significant effort,” and the company “will have to be monitored closely,” said the report, which was written by Carlo de Notaristefani, a manufacturing expert who has overseen production of Covid-19 vaccines for the federal government since last May. Though marked as a draft, federal officials said the report was considered to be final.Ten months after his report, the plant has become a major headache for the team named by President Biden to oversee the pandemic response. The Times reported on Tuesday on a host of quality control problems, flagged in audits and investigations by AstraZeneca, Johnson & Johnson, two federal agencies and Emergent’s own quality evaluators.Federal officials ordered major changes to the plant after revelations late last month that Emergent had to jettison between 13 million and 15 million doses of Johnson & Johnson’s vaccine. It is not clear what will happen to another 62 million doses of the vaccine produced at the plant, or whether Johnson & Johnson will be able to deliver the 24 million doses it has promised to the federal government by the end of the month.So far, the Food and Drug Administration has not certified the factory to distribute any doses for public use, and the agency is not expected to do so until it conducts a thorough review, which can take weeks.Asked about the June report, a company spokesman said on Wednesday night: “Emergent’s top priority continues to be the strengthening of the supply chain for Johnson & Johnson’s vitally needed Covid-19 vaccine.”Biden administration officials insist that the government has enough doses from the other two federally authorized vaccine makers — Pfizer-BioNTech and Moderna — to cover the vast majority of the nation’s roughly 260 million adults. But federal officials are still concerned about Emergent’s problems, not only because the federal government has invested heavily in the plant, but because there may be implications for the world’s vaccine supply if the issues are not resolved.AstraZeneca was expected to fulfill the majority of the global need, but safety concerns have upended those plans. British officials said on Wednesday that people under 30 should not take the AstraZeneca vaccine, and authorities in the European Union said they had found a “possible link” between the vaccine and rare but worrisome blood clots. That makes Johnson & Johnson’s vaccine more important, experts say.Emergent was forced to discard the Johnson & Johnson doses after checks revealed contamination with a virus used in the production of the AstraZeneca vaccine. An investigation is now underway, but federal and former company officials suspect the lot was tainted because an employee moved from AstraZeneca’s section of the plant to Johnson & Johnson’s without showering and taking other precautions.Between October and January, Emergent threw away five lots of the AstraZeneca vaccine — each the equivalent of two million to three million doses — because of contamination or suspected contamination, The Times reported on Tuesday.By giving Emergent a key role in its coronavirus response, the government was counting on the company to deliver on a promise made more than eight years earlier. To ensure a domestic supply of vaccines in a pandemic, the government had awarded Emergent a $163 million contract in 2012 to ready the Baltimore plant for mass production in a crisis.But Mr. de Notaristefani wrote that Emergent had used the site primarily for smaller development projects. To make large amounts of Covid-19 vaccines, the company “will have to strengthen” its quality controls, requiring “significant resources and commitment,” he wrote.His report was based in part on a visit to the plant on June 4 last year, as well as information provided by the company and conversations with the Biomedical Advanced Research and Development Authority, the federal agency that awarded Emergent the manufacturing contract.It is unclear what action, if any, the Trump administration took in response, or whether the Biden administration reviewed the findings before the recent problems arose.Mr. de Notaristefani, a former top executive at two major pharmaceutical companies, cited “significant” personnel problems, writing that plans to increase staffing seemed “inadequate to enable the company to manufacture at the required rate.”He also noted that audits by the F.D.A. and individual companies that had hired Emergent “highlighted the need for extensive training of personnel, and strengthening of the quality function.”Nonetheless, he wrote, “the organization has the necessary experience/competence” to scale up its manufacturing. He wrote that “management is knowledgeable and appears self-confident,” and with enough government oversight, “risks can be mitigated.”At the time of the visit, Emergent also planned to make a third Covid-19 vaccine, developed by Novavax, but that company has since partnered with another manufacturer in a government-backed deal. “Offloading the Novavax program to a different facility will also help reduce the load on Emergent Bayview,” Mr. de Notaristefani wrote.Emergent is a longtime federal contractor in the area of biodefense. Sales of its anthrax vaccines accounted for nearly half the Strategic National Stockpile’s half-billion-dollar annual budget through most of the last decade, The Times reported last month. That left the government with less money for items needed in a pandemic, and last year, the stockpile’s shortage of basic medical supplies became a symbol of the government’s bungled coronavirus response.Though the original federal contract for the Baltimore plant required Emergent to demonstrate large-scale manufacturing of a pandemic influenza vaccine — envisioned by health officials as a pressure test of its abilities — Emergent had yet to do so, The Times reported on Tuesday. The company risked defaulting on the original deal, which had set a deadline of June 2020. The company also has separate agreements with the two vaccine makers worth more than $875 million.In the effort to resolve the factory’s troubles, federal officials have simplified Emergent’s mission, limiting it to only producing Johnson & Johnson’s vaccine and forcing AstraZeneca to move its production lines elsewhere. Johnson & Johnson is also now asserting direct control over the manufacturing, although the work force at the plant in southeast Baltimore remains Emergent’s.The existence of Mr. de Notaristefani’s assessment was reported earlier by Politico, but its details were not previously known. Asked about the report on Wednesday, the White House spokeswoman, Jen Psaki, said she “would have to check on the specifics.”Mr. de Notaristefani’s concerns were echoed by two former plant supervisors, who spoke on the condition of anonymity for fear of career repercussions. In interviews with The Times, they cited crushing workloads and shortcuts taken to meet unrealistic timetables.Mr. de Notaristefani noted that Emergent planned to boost the factory’s work force to nearly 300. It now has 600 workers, according to the company’s spokesman. Even so, the ex-supervisors said, employees are overwhelmed, and some are often forced to work more than 70 hours a week.A review of months of company logs obtained by The Times showed that employees repeatedly said they deviated from manufacturing standards because of a lack of manpower and shortened production times.