A Baltimore factory that rendered useless 75 million doses of a coronavirus vaccine developed by Johnson & Johnson failed for weeks to seal off a preparation area for vaccine ingredients and allowed production waste to be hauled through the area, the Food and Drug Administration said in a memorandum analyzing the plant’s operations.

The memo, posted on the agency’s website late Friday, offered the most extensive explanation to date of why regulators believe that tens of millions of doses of Johnson & Johnson’s vaccine produced at that factory must be discarded.

The F.D.A. advised Johnson & Johnson on Friday that it should throw out the equivalent of 60 million doses. That brought to 75 million the total number of doses that cannot be used because of concerns about contamination at a southeastern Baltimore plant, operated by Emergent BioSolutions, Johnson & Johnson’s subcontractor and a longtime government contractor.

The vaccine-making factory has been shut for the past two months while regulators determine the cause of contamination that ruined many doses, whether it is safe to reopen the facility, and what to do with the equivalent of at least 170 million doses of vaccine that Emergent produced for Johnson & Johnson and AstraZeneca, another vaccine developer.

The F.D.A.’s memo stated that Emergent failed to properly segregate zones in which workers manufactured vaccines developed by Johnson & Johnson and AstraZeneca in order to prevent cross-contamination that could render doses unsafe or ineffective. It was written by Dr. Peter Marks, the F.D.A.’s top vaccine regulator, and was addressed to Johnson & Johnson.

When Emergent first began producing the Johnson & Johnson vaccine in November, the memo stated, the plant’s workers weighed and readied ingredients used to produce the two vaccines in separate areas. But once the factory began full production in December, workers began weighing and clearing materials for both vaccines in a common warehouse.

At the same time, the accelerated pace of production created more waste. Emergent allowed workers to tote it through the warehouse in wheeled containers, according to the F.D.A.’s report and interviews with former Emergent workers familiar with the plant’s procedures.

That mistake is most likely to blame for Emergent’s discovery in March that a batch of Johnson & Johnson vaccine had been contaminated with a key ingredient used to manufacture the AstraZeneca vaccine, the memo stated. Emergent said weeks ago that it had discarded that entire batch, the equivalent of 15 million doses.

On Friday, the F.D.A. decided that another 60 million Johnson & Johnson doses should not be used. The agency said it considered a separate 10 million doses to be safe, effective and suitable for distribution in the United States or for export. Emergent and Johnson & Johnson have both cast the clearance of those doses as a positive development that will help fight the pandemic.

The memo said that the contamination discovered in March mostly likely occurred when workers removing waste from AstraZeneca’s production zone tainted bioreactor materials that were being readied for use in the Johnson & Johnson vaccine. Besides the 15 million doses that had to be tossed out, the F.D.A. said, another 60 million should be discarded because the same lax procedures were used in producing them and evidence of trace contamination might not have shown up in tests.

There is no evidence that even a low level of contamination “would have no impact on the safety and effectiveness of the vaccine,” the memo stated.

Even though the plant did not fully follow good manufacturing practices, regulators decided to clear 10 million doses, citing the ongoing Covid-19 public health emergency.Those batches were produced under better conditions, before “the overloading of the facility’s capacities and the transit of waste in the area that led to the cross contamination” the memo stated.

The agency also underscored the fact that regulators were concerned about Emergent’s practices before the contaminated batch was discovered. In September, it stated, inspectors cited manufacturing areas crowded with equipment and supplies, inadequate support for quality assuranceand a need to improve the flow of materials and equipment.

During a follow-up visit in early February, inspectors were troubled by the number of personnel changes and new hires, as well as the need for more consistency in following manufacturing procedures, the memo said.

The government agreed in May 2020 to pay Emergent monthly fees that as of this April, would have totaled about $200 million. A federal official said the Biden administration has not been paying the Emergent fees, which were tied to production of the AstraZeneca vaccine since about April.

After the contamination was discovered, federal officials stripped Emergent of the responsibility of producing AstraZeneca’s vaccine. If and when the factory is allowed to reopen, Emergent will only produce the Johnson & Johnson vaccine, and only under Johnson and Johnson’s direct supervision. A decision on whether the Baltimore plant can resume operations is expected in a few weeks.

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