Secretary of State Rex Tillerson said, however, that Washington would maintain diplomatic relations even though the size of the US mission in Havana would be reduced to a minimum.
"Until the government of Cuba can ensure the safety of our diplomats in Cuba, our embassy will be reduced to emergency personnel to minimise the number of diplomats at risk of exposure to harm," he said.
"This order will ensure equity in our respective diplomatic operations," he said.
Cuba's Foreign Minister Bruno Rodriguez Parrilla said he would protest the order -- which he branded "unjustified... unfounded and unacceptable" -- but did not immediately threaten further tit-for-tat action.
"By these politically motivated and thoughtless actions, the US government is responsible for the current and possibly future deterioration of bilateral relations," he said.
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US halves Cuba diplomatic staff over mysterious 'attacks'
The attacks, which US officials initially suggested could have been carried out with some sort of covert acoustic device, have affected at least 22 US embassy staff in Havana over the past few months.
Those affected have exhibited physical symptoms including ear complaints, hearing loss, dizziness, headache, fatigue, cognitive issues, and difficulty sleeping.
Tillerson said the US would "maintain diplomatic relations with Cuba, and will continue to cooperate with Cuba as we pursue the investigation into these attacks."
US relations with Havana were only fully restored in 2015 -- after a half-century Cold War breakdown -- and have deteriorated since President Donald Trump took office in January.
Last week, Tillerson said he was withdrawing more than half the personnel from the US embassy in Cuba in response to the unexplained attacks.
The US expelled two Cuban diplomats in May, and Tillerson has raised the possibility of closing the American mission in Cuba altogether over the issue.
Observers doubt that Cuba would have risked antagonising its neighbors at the end of 2016 -- when relations between the former enemies were still thawing.
And even Washington has not blamed Cuba directly, although no other suspects have been identified.
'Protect our people'
The Cuban diplomats, who were given seven days to depart, were not declared persona non grata, a US official speaking on condition of anonymity said.
"Our position ... does not presume Cuban culpability," the official said.
The US diplomats leaving Cuba are expected to be out by the end of the week, and the State Department has given the Cubans a list of which diplomats they wanted expelled.
Routine US visa operations in Havana have been suspended indefinitely, and US officials have urged Americans to refrain from visiting the island.
Parrilla told the UN General Assembly last month that his country has found no evidence to support US claims that diplomats were harmed due to attacks.
Cuba 'behaving badly'
US officials previously told reporters they believed some kind of inaudible sound weapon was used on the US staff either inside or outside their residences in Havana.
Canadians in Cuba have also been hurt, with a source close to that country's embassy telling AFP that more than five families were affected, including several children.
Cuban-American Senator Marco Rubio, an outspoken critic of the Havana regime, has demanded that, until those responsible for the attacks are found, Washington should expel the same number of Cuban diplomats as Americans it is pulling from Havana.
Washington should also consider putting Cuba back on a terror blacklist, Rubio said.
"The era of constructive engagement has been replaced by one depicting the Cuban government as behaving badly," said Paul Webster Hare, a former British ambassador to Havana and political science professor at Boston University.
Webster Hare cited a September speech at the UN General Assembly in which Trump said the United States "has stood against the corrupt and destabilising regime in Cuba."
Trump further implied that further rapprochement is on hold as he "will not lift sanctions on the Cuban government until it makes fundamental reforms."
