WASHINGTON — After weeks of conflicting signals from the Trump administration about the coronavirus, the government’s top health officials decided late last month that when President Trump returned from a trip to India, they would tell him they had to be more blunt about the dangers of the outbreak.

If he approved, they would level with the public.

But Dr. Nancy Messonnier, the director of the National Center for Immunization and Respiratory Diseases at the Centers for Disease Control and Prevention, got a day ahead of the plan. At noon on Feb. 25, just as Mr. Trump was boarding Air Force One in New Delhi for his flight home, she told reporters on a conference call that life in the United States was about to change.

“The disruption to everyday life might be severe,” she said. Schools might have to close, conferences could be canceled, businesses might make employees work from home. She had told her own children, she said, to prepare for “significant disruption to our lives.”

The stock market plummeted, cable news blared apocalyptic headlines and by the time Mr. Trump landed at Joint Base Andrews early the next morning, his critics were accusing him of sowing confusion on an issue of life or death.

The president immediately got on the phone with Alex M. Azar II, his secretary of health and human services. That call scared people, he shouted, referring to Ms. Messonnier’s warnings. Are we at the point that we will have to start closing schools? the president added, alarmed, according to an official who heard about the call.

To health officials, the message needed to change with the outbreak. “The epicenter was shifting” as the number of new cases outside China surpassed those inside, said Dr. Anne Schuchat, the principal deputy director of the C.D.C. “The issue of what this might mean to us became more important.”

From the beginning, the Trump administration’s attempts to forestall an outbreak of a virus now spreading rapidly across the globe was marked by a raging internal debate about how far to go in telling Americans the truth. Even as the government’s scientists and leading health experts raised the alarm early and pushed for aggressive action, they faced resistance and doubt at the White House — especially from the president — about spooking financial markets and inciting panic.

“It’s going to all work out,” Mr. Trump said as recently as Thursday night. “Everybody has to be calm. It’s going to work out.”

Health experts say that telling people to remain calm is an effective message in an epidemic, and it is appropriate that it come from the president. Clear, honest communication is also crucial, and the United States has at times criticized China and other governments for being less than transparent.

But from Mr. Trump’s first comments on the virus in January to rambling remarks at the C.D.C. on Friday, health experts say the administration has struggled to strike an effective balance between encouraging calm, providing key information and leading an assertive response. The confused signals from the Trump administration, they say, left Americans unprepared for a public health crisis and delayed their understanding of a virus that has reached at least 28 states, infected more than 300 people and killed at least 17.

A Very Big Deal

Mr. Azar was at his home in suburban Washington, on Friday, Jan. 3, when Dr. Robert R. Redfield, the C.D.C.’s director, called to tell him China had potentially discovered a new coronavirus. Mr. Azar, a former pharmaceutical executive who helped manage the response to earlier SARS and anthrax outbreaks, told his chief of staff to make sure that the National Security Council was aware.

This is a very big deal, Mr. Azar told him.

The Trump administration had eliminated the global health unit that had been part of the National Security Council, but within days, a team was meeting daily in the basement of the West Wing, pleading with Chinese officials to allow doctors from the C.D.C. into their country.

For weeks, the Chinese refused offers of public health cooperation. “China nice-talked it for a month,” said Kenneth T. Cuccinelli, a top official at the Department of Homeland Security who was working on the coronavirus effort. “‘Oh, well, thank you for the offer. Blah, blah.’”

On Saturday, Jan. 18, a day after the C.D.C. dispatched 100 people to three American airports to screen travelers coming from Wuhan, China, Mr. Azar made his first call to Mr. Trump about the virus, dialing him directly at Mar-a-Lago, his Florida estate. The president insisted on talking about e-cigarettes first, but Mr. Azar steered him to the virus.

Four days later, during a two-day trip to the World Economic Forum in Switzerland, the president chose to focus on the positive.

“We have it under control,” he said. “It’s going to be just fine.”

On the evening of Jan. 28, a new kind of crisis broke out in the skies.

The State Department had ordered the evacuation of the American Consulate in Wuhan and a 747 was in the air. But as it headed for the United States with hundreds of passengers who possibly carried the virus, administration officials in Washington were in a frantic scramble about where it should land.

Dr. Robert Kadlec, the assistant health secretary for preparedness and response, tried to secure some kind of military base in California, but was struggling to cut through Pentagon red tape. In a panic, his staff started booking hundreds of rooms at three hotels in the Los Angeles area, asking for full floors so they could separate potentially infected evacuees from other guests.

One idea was to land the plane at the Ontario airport outside Los Angeles, and officials went so far as to schedule, then cancel, a briefing for some members of the California congressional delegation. After hours of wrangling, and with the plane still in the air, Mark T. Esper, the defense secretary, said the plane could land at March Air Reserve Base in Riverside County, which had space to house all of the passengers.

Inside the White House, a debate broke out, centered on concerns that had become ever-present since the virus first emerged: How would the government’s actions be perceived by the public? And what would the president think?

At issue was whether to impose a federal quarantine order on the evacuees to prevent them from leaving for 14 days. Such authority had not been used since a smallpox outbreak in 1969. But officials had to find some way to make sure the passengers did not leave the base until it was clear they were not infected.

Mr. Azar pushed for the order but others were wary, concerned it could cause panic. They decided to ask the passengers to voluntarily stay at the military base. One woman balked, so California officials, who use quarantine authority more often, stepped in and forced the passengers to stay.

By the end of January, the virus was veering out of control in China, the source of 23,000 visitors to the United States each day. Any one of them could be the trigger for a new and undetected American outbreak.

Over four days in the White House Situation Room, the nation’s top public health and national security officials engaged in a fierce debate over whether to take the extraordinary step of banning travel from China.

Public health officials were initially wary. Experts have long recommended against restricting travel during outbreaks, arguing that it is often ineffective and can stymie the response by limiting the movements of doctors and other health professionals trying to contain the disease. A ban would anger China, they worried, ending any hope of cooperation with American medical teams.

Officials at the National Security Council and Department of Homeland Security argued that China had already proved unwilling to cooperate. A third group inside the White House was worried that the move would incite panic and could roil the financial markets.

By Thursday, Jan. 30, the public health officials had come around. Mr. Azar, Dr. Redfield and Dr. Anthony S. Fauci, the director of the National Institute of Allergy and Infectious Diseases, agreed that a ban on travel from the epidemic’s center could buy some time to put into place prevention and testing measures. “There was so much we didn’t know about this virus,” Dr. Redfield said in an interview. “We were rapidly understanding it was much more transmissible, that it had a great ability to go global.”

The debate moved that afternoon to the Oval Office, where Mr. Azar and others urged the president to approve the ban. “The situation has changed radically,” Mr. Azar told Mr. Trump.

Others in the room urged being more cautious, arguing that a ban could have unforeseen consequences. “This is unprecedented,” warned Kellyanne Conway, the president’s counselor. Mr. Trump was skeptical, though he would later claim that everyone around him had been against the idea. The two countries were in delicate trade negotiations. Was this the time to provoke China? he asked. And what about the consequences on the economy?

The president sided with his more aggressive aides, and announced the ban next day.

Still, Mr. Trump was publicly upbeat about the effects of the virus. At a campaign rally in New Hampshire in early February, as the World Health Organization was announcing new cases by the tens of thousands, he said of the coronavirus, “By April, you know, in theory, when it gets a little warmer, it miraculously goes away.”

In fact, the fight against the virus was already beginning to stumble.

A system used to track travelers returning from China went offline just as state officials were told to begin monitoring them. Mr. Azar said at a congressional hearing that he needed at least 300 million respirator masks for health care workers, but the national emergency stockpile, the government’s reserve of disaster supplies, held only 12 million, and many of those had expired.

And a C.D.C. coronavirus test distributed to state labs had a flawed component that led to sometimes inconclusive results, crippling the nation’s testing capacity for weeks, despite assurances by the administration that it was quickly being resolved.

Americans stranded in Japan on a cruise ship, the Diamond Princess, were finally returned home Feb. 17, but the president became enraged when he learned that 14 of the passengers had tested positive for the virus in the process of being transferred to government planes.

He later said that he was worried that bringing back people who tested positive for the virus would increase the public tally of people infected in the United States.

The month ended with a whistle-blower’s claim that workers from the Department of Health and Human Services had been sent to greet returning Americans from China at two military bases in California without the personal protective gear that is required for anyone coming into contact with potentially exposed patients. None of the workers tested positive for the virus, but the allegation shook Congress.

The president’s motorcade pulled onto the main C.D.C. campus in Atlanta just before 4:30 p.m. on Friday, passing protesters holding signs that said “Have faith in science” and “We need a vaccine against Trump.”

Ten weeks after the virus first emerged in China, the total number of confirmed cases in the world surged past 100,000 and public health experts warned darkly that the outbreak was far from over. The United States, they said, faces weeks, if not months, of uncertainty and continued disruptions in education, businesses, commerce, medicine, government and daily life.

“Time matters,” Dr. Redfield said in an interview on Friday.

Last week, Vice President Mike Pence was given control of the public messaging, and although Mr. Pence has had some mixed messages of his own — he promised more tests before they were available — the White House has since displayed more discipline. Mr. Pence holds twice daily conference calls with officials from across the country, and a virus task force he leads issues daily talking points, with comment from the health professionals, to make sure the message is consistent.

But the president still has his bullhorn. During his visit to the C.D.C., Mr. Trump told reporters that he was not inclined to let 21 people who tested positive for the virus on a cruise ship off the coast of California onto American soil.

“They would like to have the people come off,” he said. “I would like to have the people stay.” The president said he would allow health experts to make the final decision, but he made clear again where he stood.

His concern? It would increase the tally for the number of people infected in the United States. “Because I like the numbers being where they are,” the president said.

Michael D. Shear and Noah Weiland reported from Washington, and Sheri Fink from New York. Reporting was contributed by Mike Baker from Seattle; Nicholas Bogel-Burroughs and Emma Fitzsimmons from New York; Katie Thomas from Chicago; and Emily Cochrane, Zolan Kanno-Youngs, Lara Jakes and Abby Goodnough from Washington.