To federal health officials, requesting states on Tuesday to suspend use of the Johnson & Johnson coronavirus vaccine until they could investigate six extremely rare but troubling cases of blood clots was an obvious and possibly inevitable move.

But where scientists saw prudence, public health officials saw a delicate trade-off: The blood clotting so far seems to affect just one out of every million people injected with the vaccine, and it is not yet clear if the vaccine is the cause. If emphasizing the clotting heightens vaccine hesitancy and bolsters conspiracy theorists, the “pause” at the end could finally sicken — and kill — more people than it saves.

With coronavirus cases spiking in states such as Michigan and Minnesota, and worrisome new variants on the horizon, health officials know they are in a race between the virus and the vaccine — and can ill afford any downsides.

“We are concerned about heightened reservations regarding the J&J vaccine, but along with that, those reservations could spill over into public concerns about other offenses,” stated Dr. Paul Simon, the chief science officer for the Los Angeles County Department of Public Health.

Officials at the Food and Drug Administration and the Centers for Disease Control and Prevention said Tuesday that the fracture in vaccinations could last only a matter of days as they sort out what occurred, determine whether to place limits on the use of this vaccine and analyze strategies to treat clotting should it occur.

Around the nation , people who have taken the one-dose Johnson & Johnson vaccine — as well as those who have not — were left to weigh their risks, particularly women ages 18 to 48, who accounted for all six cases of blood clots.

The repercussions could be more dramatic than federal officials are bargaining for, just as they had been in Europe, where a similar clotting issue has turned the AstraZeneca vaccine into something of a pariah. There, too, officials worried that blood clotting in people injected with the AstraZeneca vaccine was extremely rare. Yet based on some YouGov poll released last month, 61 percent of the French, 55 percent of Germans and 52 percent of Spaniards believe the AstraZeneca vaccine “unsafe. ”

Its a messaging nightmare, said Rachael Piltch-Loeb, an expert in health hazard communications in the N.Y.U. School of Global Public Health. But officials had no other ethical option, ” she added. “To ignore it is to seed the growing sentiment that public health officials are lying to the general public. ”

The one-dose Johnson & Johnson vaccine was only beginning to gain traction among physicians and patients after its reputation took a hit from early clinical trials suggesting its defense against the coronavirus was not as strong as competitor vaccines made by Pfizer-BioNTech and Moderna. Before Tuesday’s pause, some patients were asking for it by name.

I knew that I wanted to get the Johnson & Johnson that the notion of it being done really appealed to me, said Kayli Balin, 22, a freelance web designer and recent graduate of Wellesley College who was scheduled to get the Johnson & Johnson vaccination on Tuesday only to have her appointment . Now she’ll find the Moderna vaccine,” she said.

But amid the blizzard of news and social media attention around the pause, those gains may well be lost, especially if the rare blood clotting feeds politically driven conspiracy theorists and naysayers, who seemed to be losing ground because the speed of vaccinations ramped up.

This is precisely the wrong situation at the wrong time in the very moment that Republicans are reconsidering their hesitancy, said Frank Luntz, an American pollster who studies messaging for Republicans, a group that has shown high levels of skepticism about the coronavirus vaccines.

Brian Castrucci, an epidemiologist and head of the de Beaumont Foundation, which studies public health attitudes, stated : “It’s an easy turn to, ‘If they kept this from us, what else have they kept from us ? ’ We need to get out in front of the very quickly. ”

The issue is getting the public to understand the relative risk, said Rupali J. Limaye, who studies public health messaging at the Johns Hopkins Bloomberg School of Public Health. She noted that the potential rate of blood clotting in reaction to the vaccine is much smaller than the blood clotting speed for cigarette smokers and for women using hormonal contraception, although the kinds of blood clots differ.

Dr. Angela Rasmussen, a virologist with the Center for Global Health Science and Security at Georgetown University, made that point Tuesday on Twitter, noting that the incidence of blood clots among those vaccinated, people taking oral contraceptives and those who have Covid-19.

Patients interviewed on Tuesday said the news gave them pause — if not for themselves, then for what it would mean for the nation ’s ability to impede the spread of this virus. Jen Osterheldt, 33, of Norwalk, Ohio, who is pregnant and got the Johnson & Johnson vaccine about a month ago, said she would take it again, but worried that others would shun it even if the pause was raised.

We could potentially be doing more damage with pulling this than we think, she said.

Officials are not “pulling” the vaccine. They are simply asking for a timeout, in effect, to work out how best to use it going forward. But that timeout is causing consternation among those eager to be vaccinated, like Polly Holland, a 23-year-old state employee in Worcester, Mass., who was set to get the Johnson & Johnson vaccine next week after scheduling her appointment on Monday morning.

She had hopes of a holiday to Washington, D.C., and of hugging her 82-year-old grandma. But on Tuesday, she received an email notifying her of the pause and telling her that she would need to wait for the Pfizer vaccine instead.

I dont think with the number being as low as it is, that they should completely stop and hold us back from getting to the next step of our lives, Ms. Holland said.

Vaccinators on Tuesday were already fielding questions from concerned patients.

Maulik Joshi, the president and chief executive of Meritus Health in Hagerstown, Md., which has given out 50,000 doses of all three vaccines without any reported major reactions, stated he had a simple message to calm patients’ fears : “It’s a great thing they have paused it, and this is science at work. ”

That is the message that public health experts say the Biden administration needs to be communicating, especially to people who are undecided about vaccinations the wait-and-see group. Surveys show that group’s biggest concern is the possibility of side effects.

In January, the Kaiser Family Foundation found that 39 percent of unvaccinated people would be less likely to bring a vaccine if they heard that some patients had serious allergic reactions to it. At exactly the same time, many Americans do not distinguish among the three vaccines being available in the United States, which could cause confusion and add to vaccine skepticism.

In Europe, the public ’s confusion within the AstraZeneca vaccine, which was connected to blood clot issues, was exacerbated for weeks as different countries made different decisions, leading to a drop in confidence in the product as well as the monitoring process. American officials should emphasize swiftness of the response here in order to shore up the public ’s confidence, said Dr. Piltch-Loeb of N.YU.

People have valid concerns about side effects and vaccines, she said. “We can talk through that. Its a lot more difficult to counter the broad, emotional sentiment of deep-state government conspiracies. ’ So by addressing issues head on and being transparent, the C.D.C. will get meaningful answers and, hopefully, people will come out on the side of ‘I still need to receive the vaccine. ’ ”

Jennifer Steinhauer, Madeleine Ngo and Hailey Fuchs contributed reporting.