"Some U.S. government personnel who were working at our embassy in Havana, Cuba on official duty ... reported some incidents which have caused a variety of physical symptoms", spokeswoman Nauert told reporters Wednesday.
The symptoms have not affected US visitors to Cuba, only State Department officials.
Trump's justification of the partial reversal included a recap of Washington's oft-stated human rights allegations against the government, and the claim that the easing of restrictions hasn't had the desired "regime change" effects desired by anti-Cuban elements on Capitol Hill.
Nauert refused, however, to expand upon what sorts of "symptoms" the "incidents" caused, what the "incidents" were, or who or how many people were involved.
The US has also since expelled two Washington-based Cuban diplomats.
Nauert declined to provide further information other than to say the symptoms were "not life-threatening".
The U.S.is investigating whether Cuban officials used a covert sonic device to cause severe hearing loss among American diplomats in Havana. It's not clear whether the device was meant as a weapon or if it also served some other objective.
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USA officials, speaking to the agency anonymously, said investigations had determined devices had been deployed either inside or outside diplomats' homes. In her cagey comments yesterday, Nauert would only refer to an "incident" in which diplomats experienced "physical symptoms". "We have worked with the Cubans to try and find out what is going on".
In 2015, President Barack Obama reopened the American embassy in Cuba in an attempt to improve diplomatic relations with the country. "Cuban territory to be used for any action against accredited diplomatic officials or their families, without exception", the statement said in Spanish.
The Cuban Foreign Ministry statement released late on Wednesday said Havana complies strictly and seriously with its obligations under the Vienna Convention on Diplomatic Relations of 1961 regarding the protection and security of diplomatic agents.
The Cuban Foreign Ministry statement also called the USA decision to expel two Cuban diplomats based in Washington "unjustified and baseless".
CBS News has learned as many as eight or nine US diplomats had their assignments cut short because of their ailments.
State Department spokesperson Heather Nauert said Wednesday that officials first learned about the "incidents" at the U.S. embassy in Cuba in late 2016.
"Cuba took this issue with the utmost seriousness and acted expeditiously and professionally in order to clarify the facts of this situation, initiating a comprehensive, priority and urgent investigation on the indications of the highest level of the Cuban government", the ministry said in the statement.