Slovakia has said it will refuse Islamic migrants and only accept Christians as the EU relocates 32,000 asylum seekers.
Muslims would not be accepted because they would not feel at home in the predominantly Christian country, interior ministry spokesman Ivan Metik said.
"We could take 800 Muslims but we don't have any mosques in Slovakia so how can Muslims be integrated if they are not going to like it here?"
The EU Commission expressed its displeasure at the announcement.
"We act here in the spirit of the treaty, which prevents any form of discrimination," a spokesman said.
However Metik denied the move was discriminatory and said it was intended to ensure community cohesion.
It is legal to prioritise Christians who are at extra risk of religious persecution, one EU source told the Daily Telegraph. However turning away Muslims because there are no mosques would be discriminatory and of dubious legality.
Slovakia is due to host 200 migrants under an EU relocation scheme after EU member states agreed to take in 32,000 asylum seekers. The scheme was made voluntary after some countries, including the UK, refused to accept quotas.
The number of migrants arriving in the EU has soared in recent months, reaching a record high of 107,500 in July alone. Most are Afghans, Syrians and sub-Saharan Africans fleeing persecution, instability and poverty.
The UN Refugee Agency (UNHCR) said, "Resettlement is greatly needed for many refugees who are at extreme risk among the world's most vulnerable groups.
"We encourage governments to take an inclusive approach while considering refugees for resettlement and should not base their selection on discrimination."