The United States on Friday cut its diplomatic presence in Cuba by more than half and warned US citizens not to visit the country because of mysterious "attacks" that have caused hearing loss, dizziness and fatigue in US embassy personnel.

The US embassy in Havana will halt regular visa operations for Cubans seeking to visit the United States and offer only emergency services to US citizens, steps that may further erode the US-Cuban rapprochement begun by former President Barack Obama.

The partial evacuation, while depicted as a safety measure, sends a message of US displeasure over Cuba’s handling of the matter and delivers another blow to Obama's policies of engagement with the Cold War foe.

The Cuban government was already dealing with several delicate matters － the aftermath of Hurricane Irma, a steep decline in aid from important socialist ally Venezuela and political transition as President Raul Castro steps down next year.

Cuba's Foreign Ministry chief for US Affairs Josefina Vidal said: "We consider the decision announced today by the US government through the State Department is hasty and will affect bilateral relations."

Vidal, in a briefing on state-run television, said Cuba was still keen to cooperate with US authorities to clarify what happened.

Officials in President Donald Trump's administration stressed the United States was maintaining diplomatic ties with Cuba.

Twenty-one US embassy employees in Cuba have been injured and reported symptoms such as hearing loss, dizziness, headache, fatigue, cognitive issues, and difficulty sleeping, the State Department said.

"Until the government of Cuba can ensure the safety of our diplomats in Cuba, our embassy will be reduced to emergency personnel in order to minimize the number of diplomats at risk of exposure to harm," Secretary of State Rex Tillerson said in a statement.

The Cuban government has denied any role and is investigating. The Federal Bureau of Investigation has been looking into the incidents, a US law enforcement official said, but so far has not determined the cause.

A senior State Department official said neither the US nor Cuban governments had been able to identify who was responsible but stressed that "the government of Cuba is responsible for taking all appropriate steps to prevent attacks on our diplomatic personnel in Cuba."

In a travel warning, the State Department bluntly said "because our personnel's safety is at risk, and we are unable to identify the source of the attacks, we believe US citizens may also be at risk and warn them not to travel to Cuba." A State Department official said most visa processing had been suspended in Havana. "Cuban applicants for nonimmigrant visas may apply at another US embassy or consulate overseas."

The State Department said the attacks on US embassy personnel had occurred at "US diplomatic residences and hotels frequented by US citizens." No tourists are known to have been injured in the attacks.