Germany’s refugee crisis is challenging the country’s main religious groups as they try to balance a welcoming attitude to the mostly Muslim migrants and concern for the welfare of the minority Christians among them.

Increasingly, accounts of Muslim migrants ganging up on Christians and other minorities in refugee shelters have raised concerns.

Germany is dealing with an influx of about 1 million newcomers from the Middle East, Asia and Africa.

Scattered media reports since last fall have spoken of radical Muslims harassing Christians and other religious minorities, making them feel threatened and under pressure to convert to Islam.

The issue got national attention in early May when five minority rights groups held a news conference in Berlin to present what they said was widespread persecution of Christians and other religious minorities in refugee centers.

Open Doors Germany, a group affiliated with the international Open Doors movement to help persecuted Christians, presented a report that said 88 percent of the 231 Christian refugees they interviewed reported having suffered religiously motivated persecution in the form of insults, death threats and physical and sexual attacks.

Some felt pressure to convert and reported that Muslims were harassing them by playing loud recordings of Quran chanting. Almost half of them said they were mistreated by security guards, who are mostly Muslim foreigners who speak the refugees’ languages.

Markus Rode, the group’s chairman, said there was an “atmosphere of fear and panic” among Christian refugees and the mainstream churches were ignoring the problem.

“I really didn’t know that after coming to Germany I would be harassed because of my faith in the very same way as back in Iran,” the report quoted one refugee as saying.

Another group, Action for Persecuted Christians, estimated that 40,000 refugees in Germany, mostly Christians, were victims of religious persecution.

“These are not isolated cases. I don’t know of any refugee shelter from Garmisch to Hamburg where we have not found such cases,” said Paulus Kurt from the Central Council of Oriental Christians in Germany.

Pastor Gottfried Martens from the evangelical Trinity Church in Berlin, which works closely with Christian converts mostly from Iran and Afghanistan, called for separate shelters for Muslims and Christians.

“When a house is burning, it’s not enough to talk about fire prevention measures,” he said. “You have to pull the people out.”

The Open Doors Germany report said the authorities should register the religious affiliation of refugees and provide separate housing for Muslims and for Christians and other religious minorities. It also called for more non-Muslim security staff.

Although the news conference attracted media attention, leading German news outlets soon questioned the report’s methodology and the neutrality of the speakers. Der Spiegel newsweekly said Open Doors Germany “is controversial because it is close to the evangelicals and therefore not nondenominational.”

After those news reports were published, the Catholic bishops conference said it had surveyed its dioceses around Germany for information about the refugee situation.

“This survey suggests that intimidation and discrimination (including violence) against Christians in refugee centers are not a common problem, but they do come up repeatedly and need to be taken seriously,” it said in a statement. “The bishops conference does not think it is possible to quantify the problem.”

Berlin’s Protestant Bishop Markus Droege said his church took reports of religious persecution of Christians very seriously but did not see a general hostility to them in refugee centers.

A spokesman for the Evangelical Church in Germany, the national association of Protestant churches, rejected the idea of separate shelters according to religion. “In Germany, there must be religious freedom everywhere and for everyone, and guaranteed by the state,” he said.

The insistence by the main churches on helping all refugees without stigmatizing some of them has irritated the far-right Alternative for Germany, which has stoked suspicion of Islam to gain support among Germans concerned about the influx of refugees.

A war of words broke out after the party was not invited to attend the Catholic Assembly in Leipzig last month (May 25-29), a large festival that includes panel discussions between Catholic leaders and prominent politicians.

Alternative for Germany chairwoman Frauke Petry accused the churches of not doing enough for Middle Eastern Christians.

“Some leaders of German churches speak out more for Muslims than for their co-religionists,” she charged. “There is a clear imbalance here.”

Petr Bystron, the party’s Bavaria chairman, said the churches were profiting “under cover of loving their neighbor” by exploiting volunteers to care for refugees while taking in billions of euros in government subsidies for the shelters they run.

“If this was about belief and not about business, the churches must be skeptical about the influx of Muslims,” he wrote in an article for the German website of The Huffington Post. “This show of friendliness to refugees finances a gigantic welfare industry organized under the aegis of the churches.”

The two main churches dismissed the accusations as ignorant and misguided.

Apart from the refugee work of their charity branches, the main churches have joined Jewish and Muslim organizations in a project to support local interfaith initiatives that help refugees deal with bureaucracy, find homes and jobs, and learn German.

To qualify for government support, all interfaith projects must include one Muslim partner.

At the project’s launch in Berlin on Tuesday (May 31), senior Interior Ministry official Guenter Krings announced a government subsidy of 500,000 euros ($566,211) and said religious groups “make an important contribution to integrating refugees and strengthening our social cohesion.”

Abraham Lehrer, vice president of the Central Council of Jews in Germany, told the meeting that interfaith projects were more important than ever because the refugee influx challenged Germans to ask “how we can peacefully live together in this pluralistic and multireligious society.”

(Tom Heneghan is a correspondent based in Paris)