Mr. Ferrer had been in custody for nearly two months when his family was notified of the formal charge against him. The announcement came after criticism of his detention from across the political spectrum in the United States, including from former Vice President Joseph R. Biden Jr. and Secretary of State Mike Pompeo.

The European Parliament last week approved a joint resolution calling for his “immediate release.”

In a very unusual statement in the official Communist Party newspaper, Granma, the Cuban government described Mr. Ferrer as a “salaried agent at the service of the United States” with a history of beating his wives. His former partners posted videos denying the latter accusation.

As a community organizer, Mr. Ferrer, who is from Santiago de Cuba in the country’s east, helped collect thousands of signatures for Project Varela, a referendum demanding greater political freedom that was presented to the Cuban National Assembly in 2002. That movement’s leader, Oswaldo Payá, died in a car accident 10 years later. Many believe he was murdered.

Mr. Ferrer was caught up in the 2003 crackdown on dissidence known as the Black Spring, and served eight years in prison. He was one of the few members of a group of 75 political prisoners who refused an offer of release in exchange for exile in Spain.

“José Daniel Ferrer could read and understand the streets of Cuba,” said José Miguel Vivanco, director of Human Rights Watch’s Americas division. “My sense is that is precisely the reason they fear this guy more than anybody else.”

Mr. Ferrer emerged from prison to found the Patriotic Union of Cuba, known as UNPACU. The organization distinguished itself by tapping into social discontent born of Cuba’s frequent food shortages and other hardships.