During an open-air Mass in the Hungarian capital, Budapest, Pope Francis urged Hungary to "extend its arms toward everyone," a call that many saw as subtle criticism of Prime Minister Viktor Orban's nationalist and anti-immigration policies.
Francis, 84, spent only seven hours in Budapest on September 12 to close an international Roman Catholic meeting before moving on to Slovakia, where he will stay until September 15.
It is the first papal trip to Hungary since Pope John Paul II in 1996.
An estimated 100,000 people attended the Mass despite the coronavirus pandemic.Before the Mass, Orban greeted the Argentinian pope at the Museum of Fine Arts and the two went into a private meeting attended also by the Hungarian president and Vatican officials.
"I asked Pope Francis not to let Christian Hungary perish," Orban wrote on Facebook.
Video footage of the encounter showed Francis shaking hands with President Janos Ader, Orban and Deputy Prime Minister Zsolt Semjen and smiling, and then the Hungarian and Vatican sides sitting apart in a cavernous room of the museum.
The Vatican said the meeting was held in a "cordial atmosphere" and lasted longer than expected -- 40 minutes.
"Among the various topics discussed were the role of the church in the country, the commitment to the protection of the environment, the protection and promotion of the family," said a Vatican statement.
Francis and Orban disagree on a host of issues, top among them migration, and Francis's limited stay in Budapest could indicate that he didn't want to give Orban's government the political boost of hosting a pope for a longer pilgrimage before the general election next spring.
Orban has frequently depicted his government as a defender of Christian civilization in Europe and a bulwark against migration from Muslim-majority countries.
In 2015, he rejected proposals to settle refugees from the Middle East and Africa in Hungary and erected a fence along Hungary's southern border to keep out asylum seekers.
Francis has expressed solidarity with migrants and refugees and criticized what he called "national populism" advanced by governments like Hungary's. He has urged governments to welcome and integrate as many migrants as they can.
Vatican and Hungarian officials have insisted Francis isn't snubbing Hungary, noting that the Hungarian church and state only invited him to close out an international conference on the Eucharist on September 12.
In his remarks during the Mass, Francis said the Christian cross "planted in the ground, not only invites us to be well-rooted, it also raises and extends its arms toward everyone."
He said Hungarians should stay true to their roots while "opening ourselves to the thirst of the men and women of our time."
In his remarks, Francis warned against a resurgence of anti-Semitism in Europe, saying it is a "fuse which must not be allowed to burn."
The pope called for Christians, Jews and people of other faiths to commit themselves to promoting greater fraternity "so that outbursts of hatred that would destroy that fraternity will never prevail."
Hungary's large Jewish population was devastated during the closing months of World War II, with more than 550,000 Jewish deaths. The vast majority were deported within a two-month period in 1944 with the assistance of Hungary's fascist Arrow Cross party, and most were sent to the Auschwitz concentration camp in Nazi-occupied Poland.
The pontiff's 34th foreign trip comes two months after a colon operation and a 10-day convalescence in hospital.
He has recently resumed holding public and private audiences and says he is now living a "totally normal life," but he is still on medication and cannot stand for long periods of time.