An inspection by the U.S. Food and Drug Administration found significant sanitation and procedural problems at the East Baltimore plant that ruined 15 million doses of the Johnson & Johnson COVID-19 vaccine.

Released Wednesday, the new documents shed light on Emergent BioSolutions’ continued lack of federal authorization to distribute the vaccine it has produced. Inspectors found cleaning and sterilization failures; lack of adherence to protocols; and potential cross-contamination in multiple areas.

The FDA has instructed Emergent to pause new production while it works with the agency to correct the documented problems. But the federal regulators did not offer a timeline as to when the corrections should be implemented.

Emergent spokesperson Matt Hartwig said Wednesday that the company would work to get the facility up to par.

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

The company, based in Gaithersburg, has received hundreds of millions in federal dollars to boost production of COVID-19 therapies and vaccines, including at the East Baltimore factory near Johns Hopkins Bayview Medical Center. That plant, built with federal money to respond to pandemics and other bio-threats, has a history of violations dating back at least a year, including insufficient employee training, a lack of standardization of quality-control measures, and a non-adherence to test procedures and laboratory control mechanisms.

Johnson & Johnson subsequently assumed control of the plant at the request of federal officials. Meanwhile, federal regulators separately paused the use of the company’s single-shot vaccine to review reports of extremely rare blood clotting found in six women.

Emergent confirmed earlier this week that it had stopped production of vaccine as the FDA did its inspection of the Bayview facility. None of the bulk Johnson & Johnson vaccine from the plant has been used, as the production line had not yet been approved by federal regulators.

All Johnson & Johnson vaccine distributed in the United States had come from a plant in the Netherlands before the move by the FDA to pause its use.

The FDA’s plant inspection was completed Tuesday, a day after an institutional shareholder filed a lawsuit in the U.S. District Court for Maryland that seeks class action status for what it alleges were false statements made by Emergent and its top officials about the company’s ability to mass-produce vaccine.

The suit alleges the comments pushed up the company’s stock price, which dropped significantly after problems with the plant came to light in media reports, including both the mistake that led to the disposal of an estimated 15 million doses of the Johnson & Johnson vaccine and the ongoing quality problems.

Despite the report’s findings, the company’s stock closed up 38 cents at $66 a share Wednesday, but its shares had been trading in the $90s in March before the ruined doses came to light and as high as $125 earlier this year.

The company also faces a congressional inquiry from the Select Subcommittee on the Coronavirus Crisis. The panel plans to probe the Bayview plant’s issues and how they affected national pandemic readiness, as well as any connections company officials may have had with the Trump administration that led to contracts worth hundreds of millions of dollars for Emergent.

The committee asked that executives supply information to the panel and appear at a hearing next month. Emergent officials say they will comply with the requests.

In a statement, acting FDA commissioner Dr. Janet Woodcock, and Dr. Peter Marks, director of the agency’s Center for Biologics Evaluation and Research, said regulators would conduct additional testing on the Johnson & Johnson vaccine that already has been manufactured.

They also acknowledged the potential dent in vaccine trust caused by the blood clotting issues and problems at Emergent.

“We know that every time an American, including members of our own families, receives a COVID-19 vaccine dose, they are putting their trust in us,” their statement read. “We are working hard to maintain that trust.”

Among the problems outlined in the agency’s inspection report, regulators said plant workers were not conducting investigations into discrepancies, and had been operating out of a building that “is not maintained in a clean and sanitary condition” and also “not of suitable size, design and location to facilitate cleaning, maintenance and proper operations.”

Quality control and cross-contamination prevention mechanisms are not followed or documented, the report continued. Products were not adequately handled and stored to prevent contamination, and equipment and utensils also were not cleaned sufficiently.

Specifically, the report found:

A cross-contamination of a “viral vaccine drug substance batch” has not been thoroughly investigated

Peeling floor paint, “rough surfaces,” and wall and floor damage did not allow for adequate cleaning and sanitation

Brown wall residue and black floor residue, paint specks and “loose particles/debris”

Due to inadequate door sizing, “operators are unable to use a pallet jack for pallets to move materials in large containers. On 4/12 and 4/13, operators were observed pushing and pulling large containers along the floor to move them from ... room and... room into the warehouse.”

Inadequate waste handling, in which “operators were observed throwing unsealed bags of special medical waste into the service elevator accessing the warehouse corridor” and “dragging used medical containers and unsealed bags ... across the floor”

An overcrowded warehouse, making it difficult to move without bumping into equipment

Improper de-gowning and showering procedures and documentation gaps

A failure of the company to have “adequately trained personnel in manufacturing operations, quality control sampling, weigh and dispense, and engineering operations to prevent cross contamination of bulk drug substances”

Dr. Joshua Sharfstein, former deputy commissioner at the FDA, said the documents show “cause for concern.”

He said the federal agency reviews not just end products but also processes and the environments where they are made. Emergent has struggled in each area, he said.

“This is a serious situation,” said Sharfstein, a vice dean at Johns Hopkins Bloomberg School of Public Health and a former Baltimore health commissioner and Maryland health secretary. “Contamination has been a major problem, they’re finding gaps in there related to quality control procedures and gaps in their ability to investigate problems.”

Emergent also operates a facility in Baltimore near the Camden Yards stadium complex. Inspection reports there also show some quality issues in recent years that required the company to make improvements, according to records obtained by The Baltimore Sun through a public records request.

All those issues could be corrected through voluntary measures taken by the company, and officials say such determinations are not uncommon for drug manufacturing plants.

The Camden facility is a finishing plant, where bulk vaccines and therapies are packaged and labeled before being shipped out for use.

The Camden plant does not handle any coronavirus vaccines but is producing a monoclonal antibody therapy for COVID patients.

The FDA inspections normally occur every two years, and the Camden plant’s last inspection was in 2019, records show. It found issues largely resolved from the previous inspection, which found such things as broken vials, residue on vials and insufficient procedures to prevent contamination of products.