Relatives said Wilman Villar Mendoza, 31, died Thursday after going 50 days without food to protest his sentence, The New York Times reported.
He became at least the second political prisoner known to have died since President Raul Castro took over from his brother Fidel in 2006.
Experts say while country is moving toward a more open economy, repression of dissent continues, the Times said.
"Human rights conditions in Cuba remain poor," said William Ostick, a State Department spokesman.
"The Cuban government continues to limit fundamental freedoms, including freedoms of speech, including for members of the press, and of peaceful assembly."
Cuba, which has denied holding political prisoners, said in a statement Friday Villar "was not a dissident nor was he on a hunger strike" and that he died of sepsis after being hospitalized.
Villar was detained Nov. 2 after participating in what his wife, Maritza Pelegrino Cabrales, called a peaceful demonstration for political freedom and human rights. Prison guards put her husband in solitary confinement after he began the hunger strike Nov. 25, she said. She was last allowed to visit him Nov. 25.
Pelegrino told Human Rights Watch government officials had harassed her for associating with Ladies in White -- a group of wives, mothers and daughters of political prisoners that protests in Havana -- and said security officers threatened to take away her daughters, ages 5 and 7.
It's impossible to determine how many government opponents are in jail because independent investigators can't visit, human rights advocates say.
The advocates point to some progress in the country, where Castro agreed in 2010 to release 52 prisoners arrested in a 2003 crackdown. The government also agreed to release 2,900 inmates last year but human rights advocates say dissidents were not released.