HAVANA, Cuba - Pope Benedict XVI prayed for freedom and renewal "for the greater good of all Cubans" before the nation's patron saint Tuesday, but the island's communist leaders quickly rejected the Roman Catholic leader's appeal for political change after five decades of one-party rule.

The exchange came hours before Benedict was to meet President Raul Castro, and possibly his brother and predecessor Fidel, behind closed doors in Havana on the pontiff's second day on the island. There were no plans to meet with Venezuelan president Hugo Chavez, in Havana receiving radiation treatment for cancer.

Days after dismissing the Marxist ideology on which the Cuban system is based, Benedict continued to gently press themes highly sensitive to Cuban government in his prayer and short speech at the sanctuary of the Virgin of Charity of Cobre near the eastern 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," the pope 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."

It wasn't long before a top official back in Havana responded.

"In Cuba, there will not be political reform," said Marino Murillo, Cuba's economic czar and a vice-president.

The pope has kept his language lofty, his criticism vague and open to interpretation, but Murillo's comments left no room for doubt, and they were quickly picked up by pro-government blogs and on Twitter accounts.

Raul Castro has said that opening up Cuba's political system would inevitably spell doom for its socialist project since any alternative party would be dominated by enemies across the Florida Straits and beyond.

Alfredo Mesa, a Cuban-American National Foundation board member whose trip to Cuba was organized by the Miami Archdiocese, said the government's strong reaction would reinforce the pope's message and the need for change.

"I'd rather have them say this now than tomorrow," Mesa said.

During a quiet moment at the shrine of the Virgin of Charity, Benedict also prayed for more Cubans to embrace the faith in a country that is the least Catholic in Latin America. While most Cubans are nominally Catholic, fewer than 10 per cent practice the faith.

The pontiff knelt before the crowned, wooden statue, which stood on a covered table shrouded in blue and white cloth. Helped by two bishops, the 84-year-old pontiff rose and approached the icon, lit a candle and stood in prayer as a choir sang hymns.

He called on all Cubans "to work for justice, to be servants of charity and to persevere in the midst of trials."

The pope pointedly referred to the Virgin by her popular name, La Mambisa, in a gesture to the many non-Catholics on the island who nonetheless venerate the statue as an Afro-Cuban deity. Mambisa is the word for the Cuban fighters who won independence from Spain at the turn of the last century.

In subtle ways, the pope has acknowledged a lack of faith in the island nation, and tried to make his trip appealing to potential believers. The visit is timed to the 400th anniversary of the appearance of the statue of the Virgin to two fishermen and an African slave in Cuba's Bay of Hipe.

Dunia Felipillo, 45, said she was proud to see the pope praying before the Virgin of Charity, even though she herself was not Catholic.

"We all ask favours of la Cachita," she said, using the Cuban slang for the Virgin, as she watched the ceremony on TV from the lobby of a Santiago hotel.

Benedict's frequent references to the Virgin also highlighted what the church shares with Cuba's nonreligious population, in contrast to his views that would spark more opposition, such as the church's position on divorce and abortion and his strong comments against Marxism.

Benedict has emphasized devotion to Mary throughout his Latin America trip, also making frequent reference to Our Lady of Guadalupe earlier in Mexico. But he has also warned the faithful in the past not to overdo it and forget that Christianity is about Christ.

Meanwhile, dissidents on the island say they still don't know the man who yelled "Down with the Revolution! Down with the dictatorship!" before the pope's Mass on Monday in Santiago.

Security agents hustled him away. Video of the incident showed him being slapped by another man wearing the uniform of a first-aid worker before security agents separated them.

"We do not know his name or his whereabouts, only that it was somewhat violent," said Elizardo Sanchez, head of a group that monitors detentions of government opponents.

He urged Cuban authorities, who have not commented on the incident, to identify the man.

Benedict seemed to walk with renewed vigour Tuesday as he greeted officials and clergy when his plane arrived in Havana. The previous evening, his spokesman acknowledged that the pope was fatigued from days of travelling in Mexico.

He was greeted on the tarmac by clergy, government officials and children who played music, danced and offered him flowers.

Ana Blanco, a 47-year-old Havana resident complained about people being told to attend a papal Mass on Wednesday in Havana, saying the pressure seemed odd in a country that in her early years taught her religion was wrong.

"Now there's this visit by the pope, and I don't agree with giving it so much importance or making anyone go to the Mass or other activities," the office worker said. "Before it was bad, now it's good. That creates confusion."

Miami Archbishop Thomas Wenski, who led a pilgrimage of about 300 mostly Cuban-Americans to the island for Benedict's visit, got a sustained standing ovation Tuesday when he gave a homily in a packed Havana cathedral, calling for increased respect human rights.

Chavez sent his greetings to Benedict, but said of a meeting: "They have their agenda. I'm not going to be interfering at all."