The communist country's powerful Council of State, headed by President Raul Castro, issued the sweeping pardon in honor of the Jubilee year declared by the pope, said a front-page notice in the official communist party newspaper, Granma.
Pope Francis declared the Jubilee year last December, a special time of remission of sins and universal pardon.
Cuba said those pardoned included women, youths and sick inmates.
"The crimes for which they were punished, their conduct while fulfilling their sentences and the time served were taken into consideration," it said.
Francis kicked off the Jubilee with calls to world leaders to improve prison conditions for inmates and consider granting them amnesty.
In September last year, Cuba released 3,522 prisoners as a goodwill gesture ahead of a visit by the pope.
Cuba does not release data on its prisoner population. Anti-Castro dissidents say the figure is high for an island of 11 million people.
Authorities did not say whether any dissidents were among those pardoned. Castro's opponents accuse the regime of holding dozens of political prisoners -- something he denies.
The Catholic Church has taken on the role of mediator with the Cuban government in recent years.
That marks a rapprochement after years of tension under Castro's predecessor and older brother Fidel, the father of the 1959 Cuban Revolution.
Under Fidel Castro, Cuba was officially an atheist state from 1976 to 1992.
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