Juan Emilio Aboy surrendered himself without incident when officers arrived at his Miami home at the climax of a joint operation between the FBI and the immigration service.
The 41-year-old man is accused of spying on Cuban exiles in Florida and of trying to gain access to information from Southern Command - the branch of the US armed forces that operates in Latin American and the Caribbean.
The latest action against suspected Cuban spies by the US threatens to harm relations between the two countries further.
Deportation threat
Last December, Cuba denounced the US sentencing of a convicted spy as "despicable".
Watching brief
December 2001: US sentences Cuban to life imprisonment for spying and conspiracy to murder
February 2000: US deports Cuban diplomat accused of espionage
October 1998: Fidel Castro admits sending spies to the US
Havana described the man involved, Gerardo Hernandez, as a "national hero".
It said he was not involved in a massive spy ring as alleged, but in legitimate acts against the Cuban-American community in the US which was trying to undermine the Castro Government.
Mr Aboy faces deportation not prison.
The issue could reignite anger from earlier this month when US President George W Bush refused to lift the trade embargo on Cuba.
A statement from the US Immigration and Naturalization Service said deportation procedures had begun.
"He is an agent of the Cuban Intelligence Service and had received specific training in espionage activities and had engaged in such activities after entering the United States," the statement said.
FBI spokeswoman Judy Orihuela was reported as saying that Mr Aboy, who arrived in the US in 1996, was part of the so-called Red Wasp Network of Cuban spies who targeted military installations and Cuban exile groups in south Florida.
Mr Aboy has not been charged with espionage but is being held as a deportable alien for failing to register with the relevant authorities after entering the US.