To federal health officials, asking 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 perhaps unavoidable move.

But where scientists saw prudence, public health officials saw a delicate trade-off: The blood clotting so far appears 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 highlighting the clotting heightens vaccine hesitancy and helps conspiracy theorists, the “pause” could ultimately sicken — and even kill — more people than it saves.

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

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

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 as the rate of vaccinations rose.

The problem is explaining 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 rate for cigarette smokers or for women who use hormonal contraception, although the types of clots differ.

And officials are not “pulling” the vaccine. They are simply asking for a timeout, in effect, to figure out how best to use it.

Vaccinators were already fielding questions from worried patients on Tuesday.

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

Jennifer Steinhauer, Madeleine Ngoand Hailey Fuchs contributed reporting.

Organizers marked 100 days until the start of the Tokyo Olympics on Wednesday with a subdued ceremony amid tougher restrictions and growing questions over the event as Japan endures another surge of coronavirus infections.

The governor of Tokyo, Yuriko Koike, pledged that officials would do everything to deliver a “memorable tournament.” Wearing a mask and gloves, she unveiled statues of the Olympic mascots inside Tokyo government headquarters while a video link showed another group of officials unveiling a monument of the Olympic rings atop fog-shrouded Mount Takao, 30 miles west of the capital.

But parts of Tokyo and other municipalities remain under a quasi-state of emergency ordered last week to stem what officials describe as Japan’s fourth wave of infections. Japan has recorded nearly 3,200 infections a day over the last week, according to a New York Times database — few by the standards of the United States and Europe, but a worryingly high number for Asia.

The host nation is also lagging in vaccinations: Shots for those 65 and just began on Monday. So far, Japan has inoculated only frontline medical workers, who make up less than 1 percent of the population, and it will be far from fully vaccinated by July 23, when the Games are scheduled to begin.

Japan is calling these the “Recovery Olympics” — highlighting the nation’s recovery from the devastating earthquake, tsunami and nuclear disaster in 2011, as well as the world’s recovery from the pandemic. But the Games, originally scheduled for last year, are marching on despite more than 70 percent of the Japanese public saying they should be delayed again or called off entirely.

Organizers announced last month that international spectators would be barred, although thousands of athletes from over 200 nations are expected to compete. The ceremonial torch relay has been making its way across Japan with little fanfare; its two-day leg in Osaka this week was diverted off public roads and took place in an empty park.

First it was AstraZeneca. Now Johnson & Johnson.

Last week, British regulators and the European Union’s medical agency said they had established a possible link between AstraZeneca’s Covid-19 vaccine and very rare, though sometimes fatal, blood clots.

The pause in the use of Johnson & Johnson’s vaccine in Europe over similar concerns threatens to hurt a sluggish rollout that was just starting to gain momentum, after months of short supplies and logistical problems.

Regulators have asked vaccine recipients and doctors to look out for certain symptoms, including severe and persistent headaches and tiny blood spots under the skin. Doctors’ groups have circulated guidance about how to treat the disorder.

According to a YouGov poll published last month, 61 percent of the French, 55 percent of Germans and 52 percent of Spaniards consider the AstraZeneca vaccine “unsafe.”

Almost everywhere across the European Union, many are eager for alternatives. The Moderna and Pfizer vaccines, based on a different technology, have not been associated with similar side effects.

Although all E.U. countries have been offered a chunk of each vaccine approved in the bloc so far — AstraZeneca, Johnson & Johnson, Moderna and Pfizer — many opted to forgo parts of their share of more expensive or cumbersome vaccines like Pfizer and Moderna early on, instead favoring the AstraZeneca jab.

“In Britain or Eastern Europe, a big part of the campaigns are based on AstraZeneca,” said Yves Van Laethem, a top epidemiologist who is Belgium’s Covid task force spokesman.

Wealthier bloc members like Denmark, France, Germany and the Netherlands can better compensate for the loss of confidence in AstraZeneca, because they acquired extra doses of other vaccines — especially Pfizer — through a secondary market after poorer E.U. nations gave theirs up.

But those countries — including Bulgaria, Croatia, Latvia and Slovakia — are likely to be less able to quickly offer alternatives.

Raphael Minder contributed reporting.