Obama and Vatican worked in secret to reach deal with Cuba

The restoration of full diplomatic relations between the United States and Cuba, as well as a prisoner exchange that secured the release of American Alan Gross, was brokered, in part, by the Holy See.

A high-ranking Vatican official confirmed Wednesday that the Obama administration and the Vatican have been working together for more than a year to end decades of hostility and restore relations between the United States and the Caribbean nation.

After 18 months of secret talks hosted largely by Canada and encouraged by Pope Francis, the pontiff hosted at the Vatican the final meeting between US and Cuban officials in October, according to the Vatican. The final agreement was reached during a telephone call between Presidents Obama and Raul Castro Tuesday.

Pope Francis sent private letters to both Obama and Castro last year, the Vatican confirmed, and US officials told USA Today that Obama and the pope discussed Cuba during the president’s visit to the Vatican in March.

The pope’s involvement in the diplomacy that led to the release of Gross and a wider rapprochement between the United States and Cuba had its roots in Boston, according to the cofounder of a Cambridge-based conflict resolution group that asked Cardinal Sean P. O’Malley to talk about Cuba with the pope.

Timothy Phillips — whose group Beyond Conflict has participated in conflict resolution initiatives in Northern Ireland, South Africa, and several countries in Latin America — said his group decided to approach O’Malley about a year ago, to see whether O’Malley would be willing to ask the pope to become directly involved in efforts to normalize relations with Cuba.

Phillips said he approached Jack Connors, a Boston businessman and O’Malley confidante, who put a meeting together between archdiocese officials and Beyond Conflict last March.

“The idea was to get the pope to bring this up with President Obama when he visited the Vatican,” Phillips said. “Cardinal O’Malley was very receptive, and in the end, so was the pope.”

In his announcement of the new diplomatic relations Wednesday, President Obama thanked Pope Francis, “whose moral example shows us the importance of pursuing the world as it should be, rather than simply settling for the world as it is.”

Senator Marco Rubio, a Florida Republican whose parents emigrated from Cuba in 1956, blasted Obama for not securing more concessions from Cuba in exchange for restoring diplomatic relations — and also took a swipe at the pope’s role.

“I would . . . ask His Holiness to take up the cause of freedom and democracy, which is critical for a free people — for a people to truly be free,” Rubio, a Catholic, told Talking Points Memo. “I think the people of Cuba deserve the same chances to have democracy as the people of Argentina have had, where he comes from, as the people of Italy have, where he now lives.

“Obviously the Vatican’s its own state, but very nearby,” the senator said. “My point is, I hope that people with that sort of prestige on the world stage will take up the cause of freedom and democracy. The Cuban people are the only people in this hemisphere that have not been able to elect a leader in more than 55 or 60 years. That’s outrageous.”

But the Catholic leader of Miami, home to the nation’s largest Cuban population, praised the pope’s involvement.

“Pope Francis did what popes are supposed to do: build bridges and promote peace. He acted much like his namesake, Francis of Assisi,” Archbishop Thomas Wenski said in a telephone interview.

Still, he acknowledged that some Cuban-Americans will not be happy.

“The pain of these people is real,” he said. “They suffered, especially in the early years of the revolution, great humiliations, and often imprisonment or death — their own imprisonment or the imprisonment of relatives and loved ones — so the pain is real.”

Still, he defended the deal, and the Vatican’s involvement.

“I think basically we have to encourage [skeptics] to wait and see,” he said. “Again, the policy of confrontation and isolation after 50 years has not resulted in a change of regime, so we have to see whether a policy that starts from more engagement will lead to positive changes that will be welcome by Cubans on both sides of the Florida Strait.”

Wenski said he pressed the White House to act on Cuba during a meeting with Chief of Staff Denis McDonough in May, and called today’s announcement “just a step in what’s going to be a very long process. I think more significant things are hopefully in the future.”

Kevin Cullen of the Globe staff contributed to this report.