(CNN) The US State Department is pulling out all families of employees and nonessential personnel from Cuba, after a string of mysterious attacks against US diplomats.

Several US officials tell CNN that 21 US diplomats and family members became ill after apparent sonic attacks. The American embassy will continue to operate with a 60% reduction in staff. The officials said the US will stop issuing visas in Cuba effective immediately because of the staff reductions and the decision is not described as a retaliatory measure. Officials say there will still be consular officials in the embassy available to assist US citizens in Cuba.

The State Department is also issuing a travel warning, urging Americans not to travel to Cuba because they could also be at risk as some of the attacks against diplomats have taken place at hotels where Americans stay, a senior State Department official told reporters Friday.

"The decision to reduce our diplomatic presence in Havana was made to ensure the safety of our personnel," said Secretary of State Rex Tillerson in a written statement. "We maintain diplomatic relations with Cuba, and our work in Cuba continues to be guided by the national security and foreign policy interests of the United States."

In a statement Friday, the Cuban foreign ministry called the decision "hasty" and one that "will affect bilateral relations."

Josefina Vidal Ferreiro, the director general of the ministry's US division, said, "the Government of Cuba has no responsibility for the alleged acts and is seriously and rigorously complying with its obligations under the Vienna Convention on Diplomatic Relations of 1961, as regards the protection of the integrity of diplomatic agents accredited in the country and their families, without exception."

The statement reiterated "Cuba's willingness to continue an active cooperation between the authorities of the two countries, for the full clarification of these facts, for which a more efficient US involvement will be essential."

One senior US official said they expect the United States to ask Cuba to further draw down their personnel in Washington to voice US displeasure over the issue, but no decisions have been made.

The decision came after an exhaustive review of US diplomats' safety in Havana and discussions with the Cuban government, which has vociferously denied any involvement in the attacks.

In a meeting with Tillerson Tuesday, Cuban Foreign Minister Bruno Rodríguez denied that Cuba was involved in attacks on diplomats and said the United States was politicizing the incidents. He said his government would continue to work with US authorities investigating the attacks.

"The secretary told him independent of who is doing it, the Cubans have a responsibility for the safety and well being of our people," a senior State Department official told CNN.

At least 21 US diplomats and family members have been affected by the incidents that began in November, causing a baffling array of maladies from hearing loss to dizziness to concussions.

US officials say there may have been as many as 50 attacks, a senior US official told CNN, the most recent in August. Some victims have had long lasting symptoms and, in at least one case, permanent hearing loss.

Despite the harassment, some US diplomats told CNN they did not want to depart, saying the reductions likely played into the hands of whoever was behind the attacks and would leave the embassy understaffed during a crucial period where Raul Castro is expected to step down as president of Cuba.

Barbara Stephenson, president of the American Foreign Service Association, said the organization that represents diplomats is against the drawdown.

"Our view is that American diplomats need to remain on the field and in the game," Stephenson told CNN. "We have a mission to do and we're used to operating around the globe with serious health risks. We are not saying there aren't health hazards there. But there are health hazards everywhere and we want the same choice. "

Investigators haven't determined the cause of the incidents, but US officials told CNN they are convinced someone has targeted American diplomats in Havana with a sophisticated device never deployed before, at least not against US personnel.

Canadian diplomats have suffered similar health problems, according to US and Canadian officials.

But seven months after complaints to Cuban officials and assurances from Castro that the incidents would be investigated, US officials are frustrated by the lack of progress and have considered a range of options from scaling back the embassy to limiting the number of people who risk exposure to a full-on shuttering of the embassy, three senior US officials told CNN.

"We have to consider it. We thought we had corralled this, and then the two cases in August took place," a senior US official said. "It is not as if the attacks address individual personnel officers. Our personnel is broadly at risk. So we have to consider next steps because we need to protect our people."

A setback to US-Cuban relations

The removal of the diplomats is a setback to US-Cuban relations following the "new beginning" heralded by former President Barack Obama when he and Castro agreed to restore full diplomatic relations and to try to move past decades of Cold War tensions and mistrust. It comes at a crucial moment as Castro prepares to step down as President in February and Washington needs eyes and ears on the ground.

The Obama administration relaxed restrictions on US citizens visiting the island and, for the first time in over 50 years, re-established direct flights as well as allowing US cruise ships to travel to the island.

The State Department removed Cuba from its list of countries that support state terrorism and Obama visited the island in 2016, the first sitting US president to do since the Cuban revolution.

Some hard-liners in Cuba, including the late Fidel Castro, criticized the opening with the United States, but many Cubans rejoiced as Americans returned to the island in large numbers for the first time in a half century.

Even though he had explored opening hotels in Cuba, during the 2016 presidential campaign, then-candidate Donald Trump vowed to close the embassy if Cuba didn't agree to "a better deal" with the US.

In June, before a crowd of anti-Castro Cuban exiles in Miami, President Trump vowed to tighten restrictions on traveling and doing business with Cuba unless Havana stopped repressing human rights and political freedoms.

Trump blasted the island's government again in September in his speech before the UN General Assembly.

"The United States has stood against the corrupt and destabilizing regime in Cuba and embraced the enduring dream of the Cuban people to live in freedom," Trump said. "My administration recently announced that we will not lift sanctions on the Cuban government until it makes fundamental reforms."

More questions than answers

In November, following the US presidential election, American diplomats began to experience a series of strange incidents. As CNN first reported in August, diplomats were awoken late at night in their homes feeling unwell and hearing sounds that resembled insects or metal dragging across the floor.

They were unable to determine the source of the sound, but when they left the room or area they were in the incidents stopped immediately, two US government officials said.

By February, the State Department had concluded their diplomats were the targets of a campaign of harassment and they needed to raise the issue with Cuban officials.

The devices used in the incidents have never been found, two US officials said, but appeared to be a type of sonic weapon that emitted sound waves capable of inflicting physical harm.

But the physical symptoms that people exhibited varied greatly, preventing doctors consulted in the United States from reaching a conclusion about what caused the trauma, two US officials said.

US government technical experts were also baffled. Some affected diplomats had lines of sight to the street in their homes, while others had shrubbery and walls that blocked views of their homes. Some heard loud sounds when the incidents took place, while others heard nothing.

It does not appear either the US Embassy or the ambassador's residence were ever targeted, three senior US officials told CNN.

"Following instructions from the top level of the Cuban government, a priority investigation was opened as from the moment these incidents were first reported and additional measures were adopted to protect the US diplomats and their relatives," said a statement released by the Cuban Foreign Ministry on Tuesday. Speaking at the UN General Assembly in New York, Cuba's foreign minister Rodríguez said his government "has taken into account the data contributed by the US authorities and so far has found no evidence whatsoever that could confirm the causes or the origin of the health disorders referred to by US diplomats and their relatives."

US officials said Raul Castro denied the attacks and authorized FBI teams to travel to the island to help with the investigation, which is being led by Cuba's Interior Ministry.

Additional Cuban security guards were stationed in the neighborhoods in Havana where US diplomats live and responded within minutes when the diplomats reported a suspected attack.

US officials felt Castro would not have personally assured the Americans that Cuba had no part in the incidents if it had been a Cuban operation, a US official told CNN.

Still, US officials said the Cubans' denials strain credibility as the incidents took place in the diplomats homes and in hotels, locations that Cuba's extensive intelligence apparatus are known to closely monitor. The officials said they believe even if the Cubans didn't know about the incidents at the beginning of the investigation, they must have a clearer idea of what transpired than they are letting on.

Many diplomats live in Havana's upscale Siboney neighborhood, which has surveillance cameras and Cuban security guards posted in front of many diplomats' homes.

Top Cuban officials -- including Raul Castro -- have houses in the same area and are heavily guarded.

Other incidents took place in hotels in Havana where US diplomats were staying, said three senior US officials, also locations that Cuban intelligence services closely monitor.

"It is increasingly apparent the Cubans are involved in some way," a senior US official said. "The Cubans are all over our people while they are down there. If it was a few attacks, you could say that maybe it was the Russians or Iranians screwing with us, but when it happens so many times, especially in the same hotel, it is hard for us believe someone can get close enough to our people so many times. Unless these are beams from outer space."

After several employees who suffered attacks had to leave Havana due to health concerns, the State Department asked the Cuban embassy to send two of its diplomats home as a reciprocal measures. Earlier this month, Republican Sens. Marco Rubio, R-Florida; Tom Cotton, R-Arkansas; Richard Burr, R-North Carolina; John Cornyn, R-Texas; and James Lankford, R-Oklahoma; called on Tillerson, to declare all accredited Cuban diplomats in the United States persona non grata and, if Cuba does not take tangible action to stop the threats against American diplomats, to close the US Embassy in Havana. Rubio was a staunch opponent to the opening with Cuba under Obama and has supported Trump overturning the measures.

But State Department officials said the decision to pull out diplomats was purely a safety issue and unrelated to Washington's relationship with Cuba.

The reductions in staff will further hobble the US embassy, which is still recovering from flooding caused by Hurricane Irma. Consular services, including the issuing of visas to Cubans traveling to the US and American citizen's services department, have been closed as repairs were being made.

Several of the families of the 50 diplomats stationed at the embassy evacuated ahead of the storm and have yet to return to the island.