The US has announced that it expelled two Cuban diplomats in May after Americans working at the US Embassy in Havana suffered "unexplained physical ailments".

A small number of Americans began reporting symptoms at the end of 2016, and a few were either removed for medical treatment in the US or asked to leave, State Department officials were quoted as saying by the Washington Post on Wednesday.

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State Department spokesperson Heather Nauert linked "incidents which have caused a variety of physical symptoms" to the decision to expel two Cubans, but she did not directly blame the Cuban government for harming the Americans.

"We don't have any definitive answers about the source or the cause of the matter," she said.

A CNN report cited several senior government officials as saying that Washington believes several State Department employees at the US embassy in Havana were subjected to an "acoustic attack" using sonic devices that left at least two with such serious health problems they needed to be brought back to the US for treatment. 

Nauert also did not say how many US officials remained at the embassy in Havana as a result of the incidents or whether they have been replaced, but she did say that all of those affected are State Department personnel and not private US citizens.

Cuba's Foreign Ministry said it was investigating the allegations. It called the expulsion of its staff unjustified but said it was willing to co-operate with Washington to clarify what had happened.

"Cuba has never, nor would ever, allow the Cuban territory to be used for any kind of action against accredited diplomats or their families," the Ministry said.

One US official told CNN that the country's employees in Havana embassy could have suffered permanent hearing loss as a result.

"It can be quite serious," the official told CNN. "We have worked with the Cubans to try and find out what is going on. They insist they don't know, but it has been very worrying and troublesome."

The Federal Bureau of Investigating is looking into the matter, the report said. Further US action could follow if that investigation points to Cuban government targeting of US employees, officials said.

The State Department separately said in a statement that it had "reminded the Cuban government of its obligations under the Vienna Convention to protect our diplomats".