At the start of his first ever trip to Eastern Europe, where anti-migrant sentiments have been rising, he also encouraged Europe to welcome refugees from war, hunger and religious persecution and called for "courage" and "compassion."
Francis is celebrating World Youth Day in Poland, where the conservative government has shut the doors to migrants and many fear that accepting Muslim refugees would threaten the nation's security and its Catholic identity.
As he started the five-day trip, he told an audience of Poland's president, diplomats and other dignitaries that what is needed is "a spirit of readiness to welcome those fleeing from wars and hunger, and solidarity with those deprived of their fundamental rights, including the right to profess one's faith in freedom and safety."
While the speech had in mind the hundreds of thousands of migrants fleeing Syria, Iraq and other Mideast countries, as well as impoverished nations in Africa, his reference to practicing one's faith in safety could also be seen as an allusion to the slaying of the 85-year-old French priest by two extremists in Normandy on Tuesday.
The murder compounded security fears surrounding Francis' trip, which were already high due to a string of violent attacks in France and Germany. Polish officials say they have deployed tens of thousands of security officials to cover the event.
Francis spoke to reporters as he flew from Rome to Krakow. Asked about the slaying of the priest, Francis replied: "It's war, we don't have to be afraid to say this."
He then sought to avoid any misunderstanding of his definition of war.
"I only want to clarify that, when I speak of war, I am really speaking of war," he said. "A war of interests, for money, resources, dominion of peoples."
"I am not speaking of a war of religions. Religions don't want war. The others want war," he added.
He also reiterated earlier remarks likening the current violence to a Third War III in "segments."
In the evening, as thousands of young people cheered in the square outside Krakow's archbishop's residence in hopes of getting a glimpse of Francis, the pope's spokesman elaborated on the remarks about a world in war.
"He wanted to specify very clearly, he doesn't mean a war of religions," the spokesman, the Rev. Federico Lombardi said.
Upon arrival at Krakow airport Francis was greeted by Poland's President Andrzej Duda, First Lady Agata Kornhauser-Duda and other state officials, and hundreds of faithful who had waited for hours to see him. Prime Minister Beata Szydlo knelt and kissed his papal ring.
After a brief ceremony Francis then traveled in an open car through the city, waving at cheering crowds as he headed to the Wawel Castle for the main welcoming ceremony.
There, President Duda, a Catholic hailing from Krakow, hailed Francis as a "support, a road sign" in life for young people.
"The world today badly needs values, it needs faith and good, all of which your Holiness is bringing," Duda declared in the castle courtyard. "We are all waiting for your word."
Francis then urged Polish authorities "to overcome fear" and show "great wisdom and compassion" in dealing with migrants, whose arrivals in huge numbers on Greek, Italian and other southern European shores in the last few years has strained European nations' coffers, fueled the popularity of anti-migrant political parties and spawned fears that terrorists could show up on the continent by blending in with the refugees.
His pilgrimage will bring him later in the week to Auschwitz and Birkenau, the death camp complex run by German Nazi occupiers in Poland during World War II. Francis wants to pray silently at the sites and will also visit the place in Auschwitz where a priest gave his life to save a fellow camp inmate.
Other highlights of the pope's visit include a Saturday evening vigil with hundreds of thousands of youths who are expected to gather at a meadow, and a closing Mass on Sunday morning.