Pope Francis has urged people to welcome refugees fleeing war and hunger in his first public words after arriving in Kraków, indicating that he would not duck the issue likely to be a significant cause of tension between him and the Polish government during the five-day papal visit.

Speaking at the city’s Wawel cathedral two hours after his plane touched down on Wednesday, Francis spoke of the need for 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”.

Everything possible must be done “to alleviate the suffering while tirelessly working with wisdom and constancy for justice and peace”, he added.

There are clear points of difference on the issue of refugees between the pope and the rightwing government, headed by the Law and Justice party, which was elected last October.

Francis has made the call for compassion and generosity to refugees a hallmark of his papacy. But the Polish government has refused on security grounds to accept refugees from the Middle East.

“There are real flash points between Francis’ social agenda and the positions and comportment of the Law and Justice government, beginning with the obvious potential rift on refugees,” wrote Vatican expert John Allen on Crux, a Catholic website.

The pope is making his first visit to Poland, one of Europe’s most devoutly Catholic nations – with 93% of the population identifying with the faith and about 40% attending mass on a weekly basis.

The pontiff is celebrating World Youth Day, a week-long Catholic festival, in the company of hundreds of thousands of young pilgrims from around the world. Security in the city was at its highest possible level following the murder in France of 86-year-old Father Jacques Hamel while celebrating mass at a church near Rouen on Tuesday.

The papal jet, adorned with Polish and Vatican flags, landed at Kraków’s John Paul II Balice airport at 3.50pm. Francis was greeted by a line-up of political and church dignitaries including Poland’s president, Andrzej Duda, and the archbishop of Kraków, Stanisław Dziwisz.

Two children in Polish national dress presented him with flowers and gifts. Members of the public and pilgrims cheered and waved flags as Francis proceeded along a red carpet.

Francis travelled from the airport to Wawel cathedral in his open-sided popemobile, flanked by security vehicles, passing through streets lined with people. After welcome speeches, he prayed at the tomb containing relics of John Paul II, his predecessor-but-one and revered by the public in his home country. The pontiff also had a private meeting with Polish bishops.

More than 350,000 pilgrims from 187 countries have registered for World Youth Day in Kraków. The biggest national groups are from Poland, Italy, France, Spain and the US.

Many locals have taken holidays this week to avoid the crowds, road closures and security checks. City centre streets are dominated by large groups of pilgrims – some in national dress or religious robes, but most in shorts and t-shirts. Outbreaks of chanting and singing fuel an atmosphere reminiscent of a major football tournament crossed with a political rally.

More than 40,000 security personnel have been deployed and helicopters constantly buzz overhead.

Mobile x-ray devices and metal detectors, as well as dogs trained to detect explosives, are in use at railway and bus stations, major road hubs and venues where papal events are due to take place. Police said that gas tankers and large trucks had been banned from Kraków following the use of a 19-ton truck in a terrorist attack in Nice earlier this month.

The Polish army has a visible presence in the city centre’s main square with a display that includes tanks, a military robot, an explosion proof suit and reconnaissance vehicles.

Francis is expected to make nightly appearances on a balcony at the bishop’s palace where he is staying, to greet and interact with crowds of young people.

Maria, 25, a Pole who is studying business in Vienna, said she had returned to her homeland “to share my faith with other young people. I love Francis – he is a great man and a great pope.”

Fifteen-year-old Stephanie had travelled from Australia for World Youth Day with a school party, saying she wanted to learn more about the pope and what he stood for. “I’m here to strengthen my faith,” she added. “Here Catholicism is part of the Polish culture and national identity. It’s not like that in Australia. “He’s a modern pope and he speaks to young people.”