Women prayed at a Christmas mass on Dec. 24 in the Mar Shimoni Church in Bartella, Iraq, which had recently been liberated from Islamic State. Photo: Chris McGrath/Getty Images

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Yaroslav Trofimov, Feb. 2, 2017

Few people are more distraught by President Donald Trump’s executive order barring citizens of seven Middle Eastern and African countries from the U.S. than the leaders of a community he said he seeks to help: the region’s Christians.

Mr. Trump’s order, issued last Friday and aimed at preventing terrorist attacks on American soil, suspended travel from these Muslim-majority countries for at least 90 days. It also ordered a revamping of the U.S. refugee admission process to prioritize those who suffer religious persecution—but only if the applicants follow a “minority religion” in their country.

Most of the violence in the Middle East, however, is between Sunni and Shiite Muslims who both follow the same religion (Sunnis are a minority in Iraq and a majority in Syria). Speaking to the Christian Broadcasting Network last week, Mr. Trump said he meant to single out Christians, followers of by far the largest minority faith in the Middle East.

“They’ve been treated horribly,” he said. “We are going to help them.”

That may be good news for a few thousand Middle Eastern Christians aiming to move to the U.S.—but also a troubling message for the roughly 13 million who won’t. While White House officials reject depictions of Mr. Trump’s executive order as a Muslim ban, it has been widely portrayed in the region as consistent with his campaign rhetoric regarding Muslims entering the U.S.

“Nobody is seeing this as motivated only by security and everybody views this as targeting largely Muslim immigration,” said Basem Shabb, the only Protestant member of Lebanon’s parliament. “Trump’s offer of help is like a poisoned chalice. It has come at the expense of alienating the region’s Christians from their Muslim neighbors.”

The position of Christians in the Middle East varies dramatically. In Lebanon, where the president and the armed forces commander are both Christians, they account for a large part of the population and enjoy relative safety. In Egypt, the region’s biggest Christian community has been targeted by a series of terrorist attacks but remains a bulwark of support for President Abdel Fattah Al Sisi. Neither country is covered by the executive order.

Among the seven countries included in Mr. Trump’s ban, which prohibited entry to Muslims and Christians alike, Syria and Iraq both have large Christian communities. Christians there have been persecuted and ousted from their homes by Islamic State and other Sunni extremist groups. But they were usually afforded slightly better treatment than Shiite Muslims, who faced a choice between conversion or death.

Across the Middle East, a significant part of Muslim public opinion has long viewed Christian citizens with suspicion because of their historic links with the West. Mr. Trump’s executive order is likely to inflame these feelings, warned Michael Wahid Hanna, a specialist on the region at the Century Foundation think tank in New York.

“It paints the Christians and other minorities as almost a ward of the West, a community that doesn’t necessarily have a future in the Arab world,” he said.

That is one of the reasons why the region’s Christian leaders have denounced Mr. Trump’s move.

“Christians are part of the Middle East and they don’t accept being treated separately from their co-citizens the Muslims,” said Father Rifaat Bader, head of the Catholic Center for Studies and Media in Jordan.

Iraqi Christian leaders were particularly irate. In recent months, Iraqi forces—aided by newly formed Christian militias and by the U.S.—ousted Islamic State from most of the historic Christian heartland in Nineveh province around Mosul. Iraqi TV proudly broadcast footage of troops restoring crosses atop ancient churches.

Those advances could allow hundreds of thousands of people to return to Christian-majority towns that remained under extremists’ sway since mid-2014.

Yonadam Kanna, a Christian lawmaker who heads the minorities bloc in the Iraqi parliament, said that Mr. Trump’s executive order is likely to backfire on his country’s Christian community.

“This will lead to new discrimination. It will reflect very negatively on minorities,” Mr. Kanna said. “We appreciate the feeling of support for vulnerable communities, but what we want is to help us to stay, not to emigrate.”

Babylon Patriarch Louis Raphael I Sako, the head of the Chaldean Catholic Church in Iraq, agreed. Mr. Trump’s executive order, he said in a statement to the Vatican’s Fides news agency, is a “trap for the Christians of the Middle East” because it “creates and feeds tension with our Muslim compatriots.”

“Discriminating among those who are persecuted and who suffer based on religion ends up harming the Christians of the East,” he added. “It provides arguments for all the propaganda and the prejudices that attack Christian communities.”