Melkite Patriarch Gregory III of Damascus, Syria, said at the gathering that Christian emigration is "among the most dangerous effects of the Israeli-Palestinian conflict."
He predicted that the Christian exodus will turn Arab society into "a society with only one color, a society uniquely Muslim," the Catholic News Service reported.
Pope Benedict XVI called the two-week synod this week out of alarm over the dwindling population of Christians in a region that holds Christianity's holiest sites.
Two Muslim imams and a rabbi will address the 185 bishops from the Middle East taking part in the synod.
The synod's "working document" singled out Israel's occupation of Palestinian territories as a crucial factor for why Palestinian Christians feel so beleaguered and are apt to leave, The Associated Press reported.
Palestinian Christians are dependent on Israel for permission to enter holy sites located within Israel proper.
A few bishops also blamed radical Islamic extremists for the exodus of Christians from the Middle East.
Syrian Catholic Archbishop Basile Casmoussa of Mosul, Iraq, said that "waves of terrorism inspired by religious ideologies" as well as a decreasing Christian birthrate and an increasing Muslim birthrate are key reasons Christians are losing ground in the Middle East.
Iraq's Catholic population dropped from 2.89 percent of the country in 1980 to 0.89 percent last year. The share of Catholics in Israel's population decreased from 3.8 percent in 1980 to 1.82 percent last year.
Patriarch Gregory III, Damascus archbishop of the Greek-Melkites, an Eastern Rite church that answers to Rome, said extremist groups like Hamas and Hezbollah stemmed from the Israeli-Palestinian conflict.
"Should the East be emptied of its Christians," he said, "this would mean that any occasion would be propitious for a new clash of cultures, of civilizations and even of religions, a destructive clash between the Muslim Arab East and the Christian West."
American Cardinal John Foley, a Vatican fundraiser, singled out Israeli policies as the driving reasons behind Christian alienation in the Middle East.
"While many including the Holy See have suggested a two-state solution to the Israeli-Palestinian crisis, the more time passes, the more difficult such a solution becomes, as the building of Israeli settlements and Israeli-controlled infrastructure in East Jerusalem and in other parts of the West Bank make increasingly difficult the development of a viable and integral Palestinian state," he said, according to the AP.
But author and TV host Rabbi Shmuley Boteach, who calls himself "America's rabbi," said he was incredulous at the sentiments expressed at the synod.
"Blaming Israel for Christians leaving is one of the dumbest things I've ever heard," Boteach told AOL News. "Israel is responsible for all the freedoms in the Middle East. Israel loves Christian visitors.
"Imagine if all the Jews gave up and left Israel tomorrow and decided to all go live in Malibu," Boteach added. "Would homosexuals in the Middle East still be killed? Would there still be honor killings of a sister by her brother? Would Christian churches suddenly open in Saudi Arabia? Would the Taliban suddenly have multistate meetings? The blame for Christians leaving lies in the totalitarian regimes that trample on religious rights and are discriminatory and xenophobic."
But Tim Wallace-Murphy, author of "What Islam Did For Us," said Israel has "polarized" the Middle East.
Hares Chehab, secretary general of Lebanon's National Committee for Islamic-Christian Dialogue, said it was more than a problem and called it a "deadly dilemma."
"They must choose between disappearance and isolation, which would bring an end to their historical role and their mission," said Chehab, who also cited the Israeli-Palestinian conflict as the root of the Christian exodus from the region.
Chehab, a papally appointed observer at the synod, spoke at the gathering Tuesday.
If the Middle East is viewed as Muslim and the West as Christian, "any occasion would be propitious for a new clash of cultures, of civilizations and even of religions -- a destructive clash between the Muslim Arab East and the Christian West," Chehab said.
"To make peace, this is the great challenge. This is the great 'jihad' and the great good," Chehab said. He used the word "jihad," the Arabic word for "struggle."