There is "fear and panic" among non-Muslim refugees in Germany, it was said on Monday, as human rights organisations warned that up to 40,000 Christian and other religious minority refugees in are being harassed for their faith.

The organisations, which include the German branch of Christian persecution charity Open Doors, interviewed 231 Christians who had arrived in Germany from Iraq, Syria and Afghanistan.

Of the 231, 32 per cent said they had received death threats, and 37 per cent said they had been physically injured. Almost half said they had experienced discrimination and harassment by guards at refugee centres, and 88 per cent said they were harassed by Muslim refugees because of their faith.

According to Deutsche Welle, a protestant minister from Berlin said that Christian refugees who refused to take part in Islamic prayer were threatened.

Head of Open Doors Germany, Markus Rode, warned that the results of the survey were just "the tip of the iceberg".

The six human rights organisations at a press conference yesterday urged German Chancellor Angela Merkel to "address this intolerable situation of serious human rights violation" immediately.

It is not enough to only address religious freedom violations overseas, Open Doors Germany said in a statement. "If Christian refugees and other religious minorities in Germany are looking for protection from religious persecution and are equally discriminated against and persecuted... as in their Islamic countries of origin... this is a blatant disregard of the right to religious freedom".

The organisations called for German authorities to take religion into consideration when housing refugees.

Similar calls have been made in Sweden, where activists have warned that Christians and other religious minorities are also being persecuted.

According to the Swedish Evangelical Alliance, one Christian refugee in Kalmar, south-eastern Sweden, was threatened with "slaughter", and having his throat cut by a man who claimed to have fought with jihadist groups in Syria. A Pakistani Christian couple moved into a church when the husband's name was sprayed on a wall near their room calling for his death. A separate group of asylum seekers in Kalmar were forced to leave their accommodation when their harassment escalated.

Speaking to journalists yesterday, Syrian refugee Fadi said he fled his home country to escape from Islamist extremists, but was shocked to find Muslim fundamentalists were living in his accommodation when he arrived in Germany.

Germany accepted more than one million refugees in 2015, and remains the recipient of the largest number of asylum applications, according to the UNHCR. Merkel has faced both praise and criticism for welcoming so many people fleeing violence and persecution.