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.

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