The meeting followed Cardinal Jaime Ortega's successful mediation between Communist authorities and female relatives of imprisoned dissidents earlier this month.
That resulted in the group, known as the Ladies in White, resuming Sunday marches along a main Havana avenue free from harassment by government supporters.
"During the meeting various issues of mutual interest were analyzed, in particular the favorable development of relations between the Catholic Church and Cuban state and the current international and domestic situation," the official media said in a communique.
It was accompanied by photographs of Castro with Ortega and the head of the Catholic Bishops Conference, Archbishop Dionisio Garcia.
The Vatican's foreign minister, Archbishop Dominique Memberti, is due to visit the island next month amid increasing economic difficulties and international attention on human rights abuses in Cuba.
Dissident hunger striker Orlando Zapata Tamayo died in February and another, Guillermo Farinas Hernandez, has been hospitalized since March.
Memberti is expected to press authorities to release political prisoners whom the government brands as mercenaries and subversives in the pay of the United States.
"This is the first time the conference has had such a high level meeting," Jose Feliz Perez, spokesman for the bishops conference, told Reuters.
"It was especially relevant in the context that the church has recently been working to mediate solutions to a number of difficulties in society."
In an April interview with the Archdiocese of Havana's magazine, Palabra Nueva (New Word), Ortega said economic woes and accusations of human rights abuses had placed Cuba in "a difficult situation, the most difficult we have experienced in the 21st century."
He criticized authorities for moving too slowly on economic reforms and mistreating dissidents. But he also said the international reaction to human rights abuses was overblown and aggressive.
Laura Pollan, leader of the Ladies in White, termed the meeting "very important" in the context of the efforts to free jailed dissidents and Memberti's visit.
"If only all this could prove successful and lead to the freeing of prisoners," she said.
Relations between the Church and Cuba's government have been marked by bitter recriminations in the past, but have steadily improved since the 1990s, especially after a visit by Pope John Paul II in 1998.
SIC: Reuters