Philip J. Trapskin, the program director of Medication Use Strategy and Innovation at UW Health, the University of Wisconsin-Madison’s health system, said such actions pose a risk to patients and said he had instructed his staff to find other suppliers. Otherwise, he said, with about 2,500 nurses in his health care system who might need to use the syringes, “We’re kind of setting them up to fail if we give them something that is cracked and compromised.”

In an interview, Pfizer executives said that while the company regretted the effect the shortages were having on patients, it was investing significant resources in getting the plants up to par after taking them over from Hospira. The company plans to spend $800 million by the end of this year, and has pledged to invest at least $1.3 billion over the next five years. “We are completely aware of the essential nature of our portfolio,” said Navin Katyal, the general manager for the Pfizer Injectables unit in the United States. “The patient is truly our North Star. It’s driving our urgency to recover.”

Mr. Katyal also said that while many supplies won’t return to normal until next year, Pfizer is continuing its manufacturing — albeit at a slower pace — while the plants are being fixed and some of the most critical shortages are expected to be eased by the end of the year.

The current state of drug shortages doesn’t look that bad by the numbers. According to a recent report by the F.D.A., the agency said it had tracked just 39 new product shortages in 2017, compared with a peak of 251 in 2011. And while the F.D.A. described 2017 as a “challenging year,” it also said it had successfully prevented shortages of 145 products by taking actions such as allowing imports of certain products.

But Erin Fox, who tracks drug shortages at the University of Utah, said the figures don’t reflect the intensity of the gaps in supplies. “We’ve had all of these shortages before at different times, but what’s harder about it right now is that it’s all at once,” she said.

Dr. Scott Gottlieb, the F.D.A. commissioner, acknowledged in an interview that while the agency has made progress, it has not solved the underlying problem, where manufacturers earn a slim margin on products that are difficult to produce. “We are still in the position of trying to put a Band-Aid on a market that fundamentally hasn’t changed,” he said.

Dr. Gottlieb said he planned to act shortly on a recent request by members of Congress to look more broadly at the issue. One action, he said, could involve imposing more requirements on manufacturers, while at the same time working with programs like Medicare to increase reimbursement for certain drugs, as when they are used in outpatient clinics.