WASHINGTON — The Trump administration is poised to permanently extend the drastic cuts it made to the United States diplomatic staff in Cuba last fall after mysterious incidents in which 24 Americans were injured there, State Department officials said.

The staff reductions would have a major impact on U.S. diplomacy toward Cuba, the officials said, obscuring Washington’s view of a historic political transition on the island and limiting the contacts of American diplomats with Cuban officials, political dissidents and others. U.S. officials said the State Department has already informed the Castro government that it will likely not meet its annual commitment to admit at least 20,000 Cubans under a 1994 migration agreement. That deal was meant to discourage Cubans from trying to reach the United States aboard homemade rafts and boats.

Officials said a decision memorandum that was sent to Secretary of State Rex Tillerson last week included a proposal to keep only the emergency staff of 18 diplomats who have been assigned to Havana since the temporary reassignment of about 25 others last September. Under the department’s regulations, it has until March 4 to either send some diplomats back to their posts or reduce the staff indefinitely.

The State Department’s chief spokeswoman, Heather Nauert, said Tuesday that the department was still weighing what to do about staffing the Havana embassy. “We haven’t made a decision just yet,” she said.

Most of the diplomats who were ordered out of Havana did not want to leave. In a private letter obtained by ProPublica, 35 diplomats and spouses who worked in the embassy appealed to senior State Department officials just before the withdrawals to be allowed to remain in Cuba if they chose.

“We are aware of the risks of remaining at Post,” the group wrote on Sept. 21. “And we understand that there may be unknown risks. We ask that the Department give us the opportunity to decide for ourselves whether to stay or leave.”

A State Department spokesperson declined to comment directly on the letter. But last October, responding to earlier reports that some diplomats in Havana did not want to leave their posts, Nauert said she understood that they “believe firmly in our mission” and wanted to remain. “However,” she added, “when our Secretary looks at the situation and says, ‘We can’t protect you because we don’t know what is causing this, and we don’t know who is responsible,’ he has to make that decision to bring our folks home.”

Several diplomats first reported hearing strange, high-pitched sounds in their homes at the end of 2016, just after the election of President Donald Trump signaled an end to the rapprochement between the two countries under the Obama administration.

The first four people who came forward, ProPublica reported recently, were all intelligence officers working under diplomatic cover. Shaken by the noises, which in some cases seemed almost like beams of sound, they and others in the embassy assumed some kind of high-tech harassment by the Cuban security forces.

But the Cuban government — which has appeared strongly committed to better relations with the U.S. (and the surge of tourism and investment that came with them) — has vehemently denied any involvement in the incidents. Over the past year, Cuban officials have said they would do whatever they are asked to stop the problem, and U.S. national security officials say that Cuban authorities have cooperated closely with FBI agents who visited the island to investigate. Their inquiry has turned up no evidence to implicate the Cuban government, officials who have been briefed on it said.

Despite that, Trump administration officials have blamed Cuba for failing to protect the diplomats, arguing that the government of President Raúl Castro has such control over life on the island that it would be impossible for any attacks to take place without its knowledge.

The State Department issued a formal warning that Americans could be at risk if they traveled to the island. It also ordered 17 of the 26 Cuban diplomats in Washington and their families to leave the country. Those forced out included members of the commercial section, which worked with U.S. businesses seeking to invest in Cuba, and all but one of the embassy’s four consular officers.

The flow of American tourists has declined substantially since last summer, a change that has been felt especially by Cubans who rent out rooms to travelers, operate small restaurants called paladares, or run other small businesses that depend on such visitors.

“The travel warning has been devastating to the Cuban entrepreneurs who had benefitted from the policy of travel and openness,” said Sen. Jeff Flake, the Arizona Republican, who visited the island in January. “That’s who we say we want to help, and they’re dying on the vine.”

Flake, a longtime proponent of greater engagement with Cuba, had traveled to Havana in August 2015 to attend ceremonies for the reopening of the U.S. Embassy, 54 years after President Eisenhower severed relations. When Flake returned to Havana in this year, he said in an interview with ProPublica, he found the modernist glass-and-concrete chancery building sadly empty. “It was devastating to see basically just a skeletal staff,” he said.

State Department officials said that the emergency staff is capped at 18 — but the embassy has been run of late by as few as 11 or 12 diplomats. That’s roughly the number that Fidel Castro tried to impose in 1961, when he complained that the embassy had become “a nest of spies” trying to subvert the revolution. (Eisenhower said then that such a small staff would “render impossible the conduct of normal diplomatic relations.”)

At a potentially critical moment of political transition in Cuba — Raúl Castro has said he will relinquish the presidency in April — current and former U.S. diplomats voiced concern that Washington will lose insight as well as its growing influence.

“It’s really essential to see what’s happening in Havana and around the country in order to understand where Cuba is headed,” said Vicki Huddleston, who headed the U.S. mission in Havana from 1999 to 2002. “Essentially we’ve gone from the largest diplomatic presence in Cuba to a very small and isolated one.”

Brian Latell, a retired CIA analyst of Cuba who now teaches at Florida International University, cautioned that the two countries could still conduct diplomacy, and that it’s hard to predict how much Washington’s understanding of Cuba would be impaired by a much smaller staff. But he suggested that the big picture was already clear: “The bilateral relationship is restored to some of the darkest days of the cold war.”

A prominent Cuban dissident, Marta Beatriz Roque, said the U.S. withdrawal had already had a “dramatic” impact on human rights advocates on the island, all but eliminating their access to American diplomats and making it much more difficult for dissidents to travel to the U.S.

“Basically, I would say the interaction with the U.S. Embassy right now for us is at a level of zero,” she said in a telephone interview from Havana. “The embassy is not getting the information it needs about the human rights situation in Cuba. Our contact before was frequent. Now there is no contact.”

Roque said that during a recent trip to the U.S., she described those circumstances to Cuban-American representatives in Congress, including Sens. Marco Rubio of Florida and Bob Menendez of New Jersey, both of whom have supported the cutback. “Everybody was aware of the problem, but nobody gave me a solution,” she said.

Asked about such concerns, Rep. Mario Díaz-Balart, a Florida Republican, said the U.S. Embassy in Havana “has long been a lifeline, and important symbol, to the democratic opposition.” In a statement, he added, “It is imperative that the United States continue its solidarity with the Cuban people in their democratic aspirations.”

Consular activity at the embassy has ground almost to a halt, State Department officials said. With just one or two officers covering emergencies for visiting Americans and visas for Cuban officials, thousands of Cubans seeking to visit or immigrate to the U.S. have been forced to travel to third countries to submit their requests at American consulates there.

After months in which the U.S. Embassy in Havana issued more than 800 immigrant visas each month, the number fell to 168 in September and only 16 in October, according to State Department statistics. In November, it rose again to 196 and in December it was 22.

Cubans who want to apply for an immigrant visa to the U.S. must now do so at the U.S. Consulate in Bogota, Colombia, an additional step that Cubans have said typically costs them hundreds or thousands of dollars more in travel costs. It has prompted a chorus of complaints from people in Cuba, where the official average monthly salary is about $25, supplemented by subsidized food and free health care and education. Nonetheless, the number of visas issued rebounded to 883 in January, after the Bogotá process was fully implemented.

Some State Department officials said the visa-processing delays could be substantially remedied even with a reduced consular staff in Havana, but they added that the State Department and immigration authorities have still not produced any plan to do so.

If the department’s travel warning is extended along with the so-called ordered departure of the embassy’s non-emergency staff, educational officials said it would likely force the cancellation of about half of the U.S. college and university foreign-study programs that have been established in Cuba, because of their inability to obtain insurance.

On Thursday, an alliance of 28 American tour operators and educational travel groups called on the department to downgrade its travel warning for Cuba from its current Level Three (“reconsider travel”) to a Level Two (“exercise increased caution”), asserting that there are no confirmed cases of private American citizens in Cuba being affected like the injured diplomats. The State Department has said it has been contacted since last September by 19 American tourists who have reported having felt similar symptoms after travel to Cuba, but it did not investigate or verify any of those cases. The tour alliance also noted that Cuba was voted the “safest country in the world” for travel at the recent Madrid International Tourism Fair.

Although human rights and migration have long been top-priority issues for Cuban Americans in South Florida and other parts of the United States, the impact of the embassy staff cuts have prompted relatively little political outcry thus far.

Political analysts said the muted response may partly reflect the fact that the travel obstacles disproportionately affect a more recent (and less politically established) generation of Cuban immigrants. William LeoGrande, a specialist in U.S. foreign policy towards Latin America at American University in Washington, D.C., noted that Cuban Americans and others may also have avoided criticizing the withdrawal because of the circumstances that precipitated it.

“When people on the street in Miami realize that their relatives can’t come and visit or can’t migrate because there’s no consular section at the U.S. Embassy, that has to have a political impact,” he said. “But U.S. personnel were thought to have been attacked, and we still don’t know who did it. So, I think people don’t want to be out in front of that when they think that it could maybe have been the Cubans.”

In a Feb. 15 article in the Journal of the American Medical Association, specialists at the University of Pennsylvania’s Perelman School of Medicine found that 21 of the injured Americans had suffered a potentially “novel” type of mild brain injury caused by an unknown directed force, rather than head trauma. The authors also discounted the thesis — advanced by Cuban officials and others — that the affliction might have resulted from mass psychogenic illness.

But the JAMA report did not solve the mystery. An accompanying editorial pointed out the limitations of the study, such as the fact that an average of 203 days passed before the experts evaluated patients, raising questions about whether patients who came forward later were aware of symptoms reported by earlier ones. A lack of baseline data and other information about the patients also made it difficult to exclude other potential causes for some of the ailments, the study found.

“A unifying explanation for the symptoms experienced by the US government officials …
remains elusive,” the editorial said.