The FBI is now looking into the matter, the officials said.
"It's very strange," one official said.
State Department spokeswoman Heather Nauert on Wednesday said that "some US government personnel" working at the US embassy in Havana, Cuba on official duty reported some incidents that were causing "physical symptoms." But she could not elaborate on the nature or cause of the incidents.
"Because there are a variety of symptoms, there could be a variety of sources," one US official said. "That is why we are being very careful here with what we say. There is a lot we still don't know."
For years US diplomats in Havana complained that they suffered harassment from Cuban officials and frequently had their homes and cars broken into. But diplomats said that after the US and Cuba restored full diplomatic ties in 2015, the campaign of harassment stopped.
Some of those affected chose to return to the US, said Nauert, prompting the administration to expel two Cuban diplomats from the embassy in Washington in May.
"The Cuban government has a responsibility and an obligation under the Geneva convention to protect our diplomats," Nauert told reporters, "so that is part of the reason why this is such a major concern of ours."
"We felt like we needed to respond to the Cubans and remind them of their responsibility under the Vienna convention," one of the officials said. The officials were not declared "persona non-grata" and may be allowed to return back to the United States if the matter is resolved.
Those affected were State Department employees, Nauert said, and no American civilians were affected. The State Department is taking these incidents "very seriously," she added, and is working to determine the cause and impact of the incidents.
A Cuban government official denied any Cuban involvement in the mistreatment of US diplomats in Cuba, and said the expulsion of Cuban diplomats was an "overreaction".