Dr. Marks said the federal government hadn’t issued an order to suspend the vaccine, adding that health care providers could decide that for a given patient, the benefits of a shot outweigh the risks. “We’re not going to stop this provider from giving the vaccine because it might be right,” he said.

The decision is a new blow for Johnson & Johnson. Late last month, the company discovered that employees at a subcontracted facility in Baltimore had accidentally contaminated a batch of vaccine, forcing the company to throw away the equivalent of 13-15 million cans. That facility would handle the delivery of the vaccine to the US from Johnson & Johnson’s Dutch plants, which were federal certified earlier this year.

FDA certification of the Baltimore facility has now been delayed while inspectors investigate quality control issues and severely reduce the supply of Johnson & Johnson vaccines. The sudden drop in available doses sparked widespread complaints from governors and state health officials who had anticipated much larger deliveries of Johnson & Johnson’s vaccine this week than they did.

States have used the vaccine in a variety of settings, including at mass vaccination sites and on college campuses. The vaccine’s one-shot approach has proven popular, and officials have directed it to temporary, rural, and isolated communities where second-dose follow-up is more complicated.

It is common for regulators to investigate “safety signals” in new vaccines and other medical products. Very often the signals do not turn out to be critical. However, concerns about Johnson & Johnson’s vaccine echoes concerns about AstraZeneca’s vaccine, which European regulators investigated last month after some recipients developed blood clots.

Of 34 million people who received the vaccine in the UK, the European Union and three other countries, 222 had blood clots associated with low platelet levels. The majority of these cases occurred within the first 14 days after vaccination, mainly in women under 60 years of age.

On April 7, the European Medicines Agency, the main regulator, concluded that the disorder is a very rare side effect of the vaccine. Researchers in Germany and Norway published studies on April 9, suggesting that the AstraZeneca vaccine, on very rare occasions, caused people to make antibodies that activated their own platelets.