He also met with a Turkish Cypriot Muslim religious leader, part of careful diplomacy reaching out to both sides in the decades-old conflict between ethnic Greeks and Turks on the divided island.
Benedict'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 traveled to Cyprus to see Benedict and receive a working paper for the summit that will be made public 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, 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 with 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 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 recognizes it, and it maintains 35,000 troops there.
Shortly after Benedict's arrival, the Cypriot archbishop launched a harsh attack against Turkey, accusing it of ethnic cleansing and of aiming to take over the entire island.
Benedict has not responded directly to the Greek Cypriot leaders. On Saturday, he called for a "just settlement" of outstanding issues.
President Dimitris Christofias kept it up Saturday when Benedict visited him at the presidential palace in the divided capital. He urged the international community to put its larger geopolitical interests aside and pressure Turkey to reach an accord reunifying the island.
Christofias and Turkish Cypriot leader Dervis Eroglu last month resumed long-running peace talks after a two-month pause.
In addressing members of Cyprus' tiny Catholic community, the pope stressed the importance of interreligious dialogue for the Catholic community, a reference to the overwhelmingly Muslim Turkish Cypriots.
"Only by patient work can mutual trust be built, the burden of history overcome, and the political and cultural differences between peoples become a motive to work fore deeper understanding," Benedict said.
There were never any plans for the pope to travel to the Turkish north of the island but the Vatican said Benedict was interested in meeting Muslim representatives.
The brief encounter came as the pope was walking in a procession to a Mass at a church near the Green Line separating the two sides. Vatican spokesman the Rev. Federico Lombardi said Benedict stopped to greet the 88-year-old Sheik Nazim and that the encounter was "short but very nice."
Lombardi said the Muslim leader and the 83-year-old Benedict joked about their ages.
Associated Press writer Menelaos Hadjicostis contributed to this report from Nicosia.