Slovakian officials have announced 200 new refugee arrivals are expected to enter Slovakia, but that only Christians would be accepted.
Interior Ministry spokesman, Ivan Metik, spoke to the Wall Street Journal saying Muslims would not be accepted to the country because they would “not feel at home.”
"In Slovakia, we don’t have mosques," the official said.
“Therefore we only want to choose the Christians,” he added.
Babar Baloch, Central Europe spokesman for the United Nations High Commissioner for Refugees, spoke regarding the issue calling for countries to take an "inclusive approach" to relocation.
"Resettlement is greatly needed for many refugees who are at extreme risk among the world's most vulnerable groups,” Baloch said.
"We encourage governments to take an inclusive approach while considering refugees for resettlement and should not base their selection on discrimination."
Metik refused this action as discriminatory, adding the main intention was to ensure community cohesion.
EU member states agreed last month to accept 32,000 refugees arriving in Italy and Greece over the next two years, while the target was originally 40,000.
The plan was later made voluntary after some nations such as Slovakia refused to accept the already set quotas as the EU countries failed to agree on how to distribute the refugees.
European Union officials have put pressure on the country to accept migrants, while the Slovakian government, like some other Central and Eastern European states such as Estonia, Hungary and the Czech Republic, bristled at the demands.
"Left-wing policies have led to illegal immigrants flooding Europe, threatening European countries with an unprecedented social, economic, cultural and security conflict," a statement from the governing nationalist party of Hungarian Prime Minister Viktor Orban, said.
According to German DPA news agency, a group named “the Bloc Against Islam” in the Czech Republic, collected signatures for a petition against Muslim immigrants.
The European Union's border agency reported on Tuesday that 107,500 migrants crossed into the EU in July.
Syrian refugees escaping the violence in their country fled Syria with the escalation of the Syrian Civil War, in 2012, in large numbers.
Most of the Syrian refugees fleeing civil war entered neighbouring Turkey, which has pursued an "open-door" policy for Syrian refugees, to ease the humanitarian crisis that the people of Syria have been facing.
The country has accepted almost 2 million Syrians and has spent about $6 billion regarding the Syrian refugee situation, while the international community has contributed by giving only around $300 million, the Turkish government announced in June.
The UN has said that some 250,000 people have been killed and an estimated 7.6 million are internally displaced. About 5 million others have fled the country into neighbouring Turkey, Lebanon, Jordan, Egypt, Iraq, as well as Europe.