"The world is at war, the world is suffering," the Argentine said ahead of the meeting, which came as fighting resumed in Syria and the US investigated an attack possibly linked to the Islamic State group.
"There is no God of war," he said, calling on "all men and women of good will, of any religion, to pray for peace".
The annual World Day of Prayer event, established by John Paul II 30 years ago and held in the medieval town in central Italy, aims to combat the persecution of peoples for their faiths and extremism dressed up as religion.
"We are frightened... By some terrorist acts" but "this is nothing compared to what is happening in those countries, in those lands where day and night bombs fall," he said at a morning mass at the Vatican.
"As we pray today, it would be good if we all felt shame, shame that humans, our brothers and sisters, are capable of doing this."
The Vatican said he would also meet one-on-one with unnamed Muslim and Jewish representatives, as well as Koei Morikawa, the Supreme Head of the Tendai Japanese school of Mahayana Buddhism.
Syrian Mohanad Zanboua, who was to eat with Francis along with his wife Nour and their daughter Maria, said they had fled the country at the end of 2014 "after three years of war and terror".
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