U.S. authorities accused a retired American diplomat on Monday of having worked for decades as a secret agent for the Cuban government, saying there was evidence that he had secretly supported the foreign nation while he rose up the ranks of the U.S. State Department.

In a criminal complaint filed in federal court in Miami, federal prosecutors said that the diplomat, Manuel Rocha, had secretly aided Cuba’s “clandestine intelligence-gathering mission against the United States” since 1981, and appeared to have met with handlers from Cuba’s premier spy agency as recently as 2017.

For more than two decades, Mr. Rocha handled matters related to Latin America in a series of roles at the State Department, including as the ambassador to Bolivia until 2002. More recently, he was an adviser to a U.S. military command that was responsible for Cuba, among other areas.

The complaint does not delve into details of how Mr. Rocha may have influenced American policy, or what information he may have sent to Cuba. But it describes three meetings over roughly the last year between Mr. Rocha and an undercover F.B.I. agent who Mr. Rocha believed to be a representative of Cuba’s spy agency, the Directorate of Intelligence.

Several times during those meetings, Mr. Rocha spoke of working in the interest of that agency, and he referred to the United States as “the enemy,” according to an affidavit filed in court by Michael J. Haley, an F.B.I. special agent in Miami. Mr. Rocha was quoted in the affidavit saying that “what we have done” is “enormous” and “more than a grand slam,” though the affidavit does not specify what he was referring to. The conversations were in Spanish and were translated by the F.B.I.

Mr. Rocha was charged on Monday with acting as an illegal agent of a foreign government and with two other crimes. He was expected to appear in a Miami courtroom on Monday afternoon.

In a statement, Attorney General Merrick B. Garland said that Mr. Rocha had sought positions in the diplomatic service that gave him access to secret information and allowed him to influence foreign policy.

“This action exposes one of the highest-reaching and longest-lasting infiltrations of the United States government by a foreign agent,” Mr. Garland said.

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