The pope strongly supported Croatia's bid to join the European Union, but said he understood Eurosceptics' fear of an "overly strong" centralized bureaucracy.
At the beginning of his first visit to Croatia as pope, Benedict XVI expressed the Vatican's long-standing concern that Europe must be reminded of its Christian roots "for the sake of historical truth."
The previous pope, John Paul II, visited Croatia three times during and after the wars of the 1990s.
Thousands of young Croats braved the heavy rain as they waited for the Pope to arrive for the vigil in Zagreb's main square.
"We'll stay here all night if we have to!" said Josipa Petročić, who was standing in Ban Jelačić Square in the sea of Croats who were singing and dancing, the reporter of the agency Aosišiejtid pres reported.
"We don't mind the rain, we would stay even if it was snowing because we love the pope."
The Pope's visit is a boost to the conservative government's efforts to close negotiations with the EU.
The Pope said that it is "logical, just and necessary" for Croatia to join the EU, considering that its history and culture are so strongly rooted in European ones.
"From the very beginning, your people belong to Europe and in a special way contribute to the spiritual and moral values that through the ages shape everyday life as well as the personal and national identity of its children," the Pope said upon arrival at the Zagreb airport, Croatian media reported.
The Pope, however, in statements given to journalists on the plane, admitted that fear or skepticism about joining the EU is understandable if you take into account that Croatia is small and shares different values from other, more secular EU nations.
"It is understandable that there may be a fear of an excessively strong centralized bureaucracy and a rationalistic culture that does not take enough account of history - the wealth of history that Croatia offers," he said.
"He called on Croatia to fulfill its mission of joining the EU by "promoting fundamental moral values, rooted in the social life and identity of the old continent."
The Croatian president agreed, saying that Europe would not have united if it were not for the deep Christian values of forgiveness and reconciliation that Croatia cherishes.
"The unification of Europe is fundamentally a Christian project," Josipovic said, as a military parade and Croats in traditional clothing greeted the pope at the airport.
Josipović pointed out that the pope's visit comes at an important moment when Croatia is celebrating its 20th year of independence and when accession negotiations with the EU are nearing their end.
The Vatican and Croatia, where 89,8 percent of Catholics live, have long had strong relations. The Holy See was among the first to recognize Croatia's independence and the Vatican wants another strong country to join the 27-member bloc.
Stepinac enjoyed hero status among Catholics for his resistance to communism and refusal to separate the Croatian Church from the Vatican
On Sunday, the Pope will hold a mass on the occasion of the National Day of Croatian Catholic Families and pray at the grave of the controversial Cardinal Alojzij Stepinac.
Stepinac, who led the Croatian Catholic Church during World War II, was beatified by Pope John Paul II in 1998.
The visit of the head of the Roman Catholic Church will cost Croatia around two million euros, which will be shared by the state and the church.
After the war, the communist Yugoslav authorities accused Stepinac of collaborating with the Ustasha government, which he denied, and sentenced him to 16 years in prison.
Benedikt said that Stepinac defended true humanism from both the communist dictatorship and the Ustasha regime, which "allegedly realized the dream of autonomy and independence, but in reality that autonomy was a lie because Hitler used it for his own goals."
Benedict XVI, 84, has not been abroad since visiting Spain in November, and this is his 19th trip since becoming pope in 2005.
Security measures in Zagreb have reached the highest level.
The visit of the head of the Roman Catholic Church will cost Croatia around two million euros, which will be shared by the state and the church.
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