President Castro meets Catholic Church leaders
Mr Castro met Cardinal Jaime Ortega, head of the country's Church, along with Archbishop Dionisio Garcia of Santiago.
Wednesday's talks touched on the sensitive issue of imprisoned political dissidents, Church sources said, without providing details.
This comes ahead of a visit next month by the Vatican's foreign secretary.
The official Communist party newspaper - Granma - said the discussions had covered relations between Church and state, as well as international and domestic issues.
Archbishop Garcia, the head of Cuba's bishops' conference, was cautious when asked whether the discussion might lead to an agreement to free dissidents.
"There will be a process and this process has to start with small steps and these steps will be made," he was quoted as saying by AFP. "We hope that the conversation will go in that direction."
In the early days of the revolution, Cuba officially became an atheist state, but relations with the Church have been steadily improving since Pope John Paul II's historic visit in 1998.