He had an hour-long meeting with Cuban President Raul Castro, while former President Fidel Castro has written in an article on the government’s website that he is “happy” to meet the Pope.
According to AP, Mr Castro said: "I will happily greet His Excellency Pope Benedict XVI as I did John Paul II, a man for whom contact with children and the humble generated feelings of affection."
According to reports, Cuban officials insist that there are no plans for political reform in light of the Pope’s visit.
Earlier in his visit, the Pope prayed for freedom and renewal “for the greater good of all Cubans” at the sanctuary of the Virgin of Charity of Cobre near the city of Santiago.
"I have entrusted to the Mother of God the future of your country, advancing along the ways of renewal and hope, for the greater good of all Cubans," he said.
"I have also prayed to the Virgin for the needs of those who suffer, of those who are deprived of freedom, those who are separated from their loved ones or who are undergoing times of difficulty."
His visit coincides with the 400th anniversary of the appearance of the statue of the Virgin to two fishermen in the Bay of Hipe.
Catholics account for around 10% of the population in the communist country.
Rights groups, including Christian Solidarity Worldwide, said that dissidents had been subject to restrictions on their movements around the Pope’s visit.
CSW reported that members of the Ladies in White were prevented from attending Sunday morning mass, and roadblocks were set up in some areas to prevent members of human rights or pro-democracy groups from accessing churches.
Speaking en-route to Mexico, where the Pope spent two days prior to his arrival in Cuba, he said the Church is “always on the side of freedom”.
Church officials have reportedly said that there is not enough time for the Pope to meet with dissidents before his departure later today.