NICOSIA, Cyprus — In a document presented here on Sunday by Pope Benedict XVI, bishops from across the Middle East called on Christians to become a dynamic minority in a conflict-ridden region and attributed their declining population here to “instability” caused by the Israeli-Palestinian conflict, the war in Iraq and unrest in Lebanon.

It also lamented the rise of “political Islam,” and said Christians suffered in countries where Muslims often “make no distinction between religion and politics.”

Benedict’s five-year-old papacy has been marked by tensions with Muslims and Jews, which his visit last year to Jordan, Israel and the West Bank did not entirely put to rest. The document issued Sunday, a working paper for a meeting of bishops to be held in Rome this fall, touched on some of the most contentious issues of Middle East politics and seemed poised to elicit controversy.

Ending his three-day visit to Cyprus, Benedict also made a “personal appeal for an urgent and concerted international effort to resolve the ongoing tensions in the Middle East, especially in the Holy Land, before such conflicts lead to greater bloodshed.”

His visit, the first by a pope to Cyprus, was aimed at strengthening ties between the Catholic and Orthodox churches and calling attention to the situation of Christians in the Middle East.

But even as the pope called for peace and dialogue, the weekend was darkened by the killing in Turkey on Thursday of Bishop Luigi Padovese, 62, the head of the Turkish bishops conference and one of the authors of the document. His Turkish driver has been arrested and charged with the crime. The pope has played down the killing as a “personal” matter and not driven by religious or political motives, although the details surrounding the death remain unclear.

In recent decades, the percentage of Christians in the Middle East has fallen from 20 percent of the population to less than 5 percent, and the number is dropping.

“Today, emigration is particularly prevalent because of the Israeli-Palestinian conflict and the resulting instability throughout the region,” the bishops’ document said. “The menacing social situation in Iraq and the political instability of Lebanon further intensify the phenomenon.”

It also said that the Israeli occupation of Palestinian territories created “difficulties in everyday life, inhibiting freedom of movement, the economy and religious life,” as well as making access difficult to some Christian holy sites in the West Bank, like the Church of the Nativity in Bethlehem.

Israel’s ambassador to the Vatican, Mordechay Lewy, said the document’s assessment of the situation of Christians in Israel and the Palestinian territories was “more or less realistic,” but he dismissed the idea that the Israeli-Palestinian conflict was the main cause of Christian flight.

“We reject any view which pinpoints the conflict between the Palestinians and us as the source of every instability in the region,” he said. “The region is also unstable without this conflict.”

In a passage that seemed aimed at American evangelicals, the document said that “certain Christian fundamentalist theologies use sacred scripture to justify Israel’s occupation of Palestine, making the position of Christian Arabs an even more sensitive issue.”

The Italian-language version of the passage was more critical of Israel and said that scripture should not be used “to justify the political injustice imposed on the Palestinians.”

The Vatican spokesman, the Rev. Federico Lombardi, said both versions were official. “They are rather different,” he acknowledged. “But this is a working document.”

The document was written by a dozen bishops and top Vatican officials, including the Latin patriarch of Jerusalem and bishops from Egypt, Syria and Iran, based on comments submitted by bishops across the Middle East before a monthlong bishops’ meeting in Rome in October.

Benedict sees Christians “not as a minority in decline, but as a creative minority,” said Andrea Riccardi, the founder of the Community of Sant’Egidio, a lay Catholic group active in interreligious dialogue that helped organize the pope’s visit to Cyprus. “The Christian minority in the Middle East is important to prevent Muslim totalitarianism.”

The document said relations between Christians and Muslims were often difficult “principally because Muslims make no distinction between religion and politics, thereby relegating Christians to the precarious position of being considered noncitizens, despite the fact that they were citizens of their countries long before the rise of Islam.”

But Adnane Mokrani, a Tunisian Muslim who teaches Islamic studies at the Pontifical Gregorian University in Rome, said the link between religion and politics came from “history and culture” more than Islam. “The real problem is dictatorship, which often tries to justify itself using religion and nationalism,” he said.

A version of this article appeared in print on June 7, 2010, on page A9 of the New York edition.