Pope Francis called on Saturday for an "urgent" end to the Syrian civil war and the refugee crisis it has spawned as he opened a three-day trip to the Middle East.

Francis deviated from his prepared remarks to make a strong plea for peace during his first day in Jordan, praying for God to "convert those who seek war, those who make and sell weapons!"

The appeal came during a meeting with refugees, just moments after the pontiff bent down at the Jordan River, where some believe was the site of Jesus' baptism, and touched the waters. And it capped an intense day at the start of his first visit as pope to the Holy Land.

"Vive il papa," a group of schoolchildren waving Vatican flags shouted as the pope arrived earlier on Saturday at the royal palace for private talks with King Abdullah II, Queen Rania and their children.

Francis thanked Jordan for its "generous welcome" to Syrian refugees and called for an urgent resolution to the civil war next door.

Italy Pope Mideast

Pope Francis waves to reporters as he boards a plane in Rome to Amman, Jordan, for a three-day trip to the Middle East. (Riccardo De Luca/Associated Press)

"I urge the international community not to leave Jordan alone in the task of meeting the humanitarian emergency caused by the arrival of so great a number of refugees, but to continue and even increase its support and assistance."

Jordan last month opened a third refugee camp for Syrians who fled the civil war at home, evidence of the strains the conflict is creating for the country. Jordan is currently hosting 600,000 registered Syrian refugees, or 10 percent of its population, but Jordanian officials estimate the real number is closer to 1.3 million.

"I thank the authorities of the kingdom for all they are doing and I encourage them to persevere in their efforts to seek lasting peace for the entire region," Francis said. "This goal urgently requires that a peaceful solution be found to the crisis in Syria, as well as a just solution to the Israeli-Palestinian conflict."

Francis saw the refugee exodus first-hand, meeting with some 600 Syrian and Iraqi refugees and disabled children at a church in Bethany beyond the Jordan, which many believe is the traditional site of Jesus' baptism.

Francis, who has frequently despaired over the plight of refugees, told them that he had wanted in particular to meet with them during his trip and issued a heartfelt plea for peace in their homeland.

"I pray once more that reason and restraint will prevail, and that with the help of the international community, Syria will rediscover the path of peace," he said.

Francis touched on the theme of peace during an afternoon Mass at Amman's windswept international stadium, urging the faithful to "put aside our grievances and divisions" for the sake of peace and unity.

Overhead, enormous blue balloons in the shape of a rosary, complete with a blue balloon crucifix, rose high into the sky.

"Peace isn't something which can be bought; it is a gift to be sought patiently and to be crafted through the actions, great and small, of our everyday lives," he said. The crowd, which the Vatican had estimated could exceed 25,000, gave him a warm welcome as he zipped around the stadium in his open-topped car, kissing children and youngsters who came up to him.

Christian Syrians fear being targeted

Christians make up about 5 per cent of Syria's population, but assaults on predominantly Christian towns by rebels fighting President Bashar Assad's rule have fuelled fears among the country's religious minorities about the growing role of Islamic extremists in the revolt. Christians believe they are being targeted in part because of anti-Christian sentiment among Sunni Muslim extremists and partly as punishment for what is seen as their support for Assad.

Francis has frequently lamented the plight of refugees, denouncing the "globalization of indifference" that often greets them in their newly adopted homelands. At the same time, he and his predecessors have decried the flight of Christians from the Holy Land, insisting recently: "We will not be resigned to think about the Middle East without Christians!"

King Abdullah referred to Christian-Muslim coexistence in his remarks, saying Christian communities were an "integral part" of the Middle East and that he had sought to uphold "the true spirit of Islam, the Islam of peace," which extends to protecting holy sites for Christians and Muslims alike. He urged the pope to help end the conflict in Syria and to encourage leaders to take the courageous steps needed to end the Israeli-Palestinian conflict.

"Your humanity and wisdom can make a special contribution to easing the crisis of Syrian refugees and the burden on neighbouring host countries like Jordan," Abdullah said, addressing the pope.

On the Israeli-Palestinian conflict, the king added: "The status-quo of `justice denied' to the Palestinians; fear of the other; fear of change; these are the way to mutual ruin, not mutual respect."

For the refugees who will greet Francis on Saturday, his presence in Jordan is a chance to show the world their hopelessness as the Syrian conflict drags on.

"We are very happy because he will see Christians in the Arab world, he will see us and see our suffering," said Nazik Malko, a Syrian Orthodox Christian refugee from Maaloula who will be among the 600 or so people to greet the pope at Bethany beyond the Jordan. "We wish that peace will be restored in the whole world, and in Syria."

Refugee camp visits

Francis has a packed schedule for the three-day visit: He will visit a Palestinian refugee camp Sunday when he travels from Amman directly to the West Bank city of Bethlehem. It's the first time a pope has landed in the West Bank rather than Tel Aviv first in a nod by the Vatican to the "Palestinian state."

Technically, the main reason for the trip is for Francis and the spiritual leader of the world's Orthodox Christians to mark the 50th anniversary of a historic meeting in Jerusalem by their predecessors which ended 900 years of Catholic-Orthodox estrangement. That highlight will come on Sunday, when Francis and Ecumenical Patriarch Bartholomew I preside over a joint prayer service in the Church of the Holy Sepulchre, where Christians believe Jesus was crucified and resurrected.

Francis will spend Monday in Jerusalem, visiting the grand mufti of Jerusalem and Israel's chief rabbis, albeit separately. He'll also pray at the Western Wall and visit the Holocaust memorial at Yad Vashem.

The Vatican spokesman had suggested that with such a gruelling schedule, Francis might not have the strength for an on-board press conference on the return flight from Israel on Monday night. Francis, 77, who has only one full lung and has battled a cold and fatigue that forced him to cancel some recent appointments, set the record straight at the start of the trip.

"One of you said a press conference wouldn't be possible because this is a `deathly' trip," he told reporters. "But returning home, I intend to have one."

He then greeted reporters one by one — and even posed for a "selfie."