The Pope has appealed for support for embattled Christian communities in the Middle East, calling them a vital force for peace in the region.
He also met a Turkish Cypriot Muslim leader, part of careful diplomacy reaching out to both sides in the decades-old conflict between ethic Greeks and Turks on the divided island.
Benedict XVI's three-day pilgrimage to Cyprus is part of preparations for a crisis summit of Middle East bishops in Rome in October. Many bishops from the region have travelled to Cyprus to see Benedict and receive a working paper for the summit that will be made public on Sunday.
War and harsh economic conditions have led to the exodus of thousands of Christians from the Holy Land, Iraq and elsewhere in recent years.
Later on Saturday, at an afternoon Mass, Benedict lamented that priests have joined the emigration of Christians from the region.
He said that as families leave because of conflicts and tensions, "it can be tempting for their pastors to do likewise".
Meeting Orthodox Christian Archbishop Chrysostomos II, Benedict said the continuing conflict in the Middle East "must be a source of concern to all of Christ's followers".
"No one can remain indifferent to the need to support in every way possible the Christians of that troubled region, so that its ancient churches can live in peace and flourish," Benedict said.
Benedict has walked a careful diplomatic path since arriving on Friday on the eastern Mediterranean island. Cyprus was ethnically split in 1974 when Turkey invaded after a coup by supporters of union with Greece. Turkish Cypriots declared an independent republic in the north in 1983, but only Turkey recognises it, and it maintains 35,000 troops there.
Shortly after Benedict's arrival, the Cypriot archbishop launched a harsh attack on Turkey, accusing it of ethnic cleansing and of aiming to take over the island. Benedict has not responded directly to the Greek Cypriot leaders. On Saturday, he called for a "just settlement" of outstanding issues.