A European Commission spokeswoman said late on Wednesday that Slovakia would not have the right to accept only Christian migrants.
Slovakia is due to receive 200 migrants under an EU scheme in which 32,000 people are to be resettled with each member state accepting a certain number.
However, Slovakia will only accept Christian migrants, a spokesman for the country's Interior Ministry told the BBC on Wednesday.
"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?" Ivan Metik was quoted as saying.
EC spokeswoman Annika Breidthardt was quoted in U.K. newspaper The Telegraph, warning that discrimination of any kind would not be tolerated under its scheme.
Most migrants have arrived from countries with large Muslim populations in North Africa and the Middle East.
Metik maintained that the policy was not discriminatory, claiming that migrants would not wish to remain in Slovakia in any case.
Slovakian Prime Minister Robert Fico told Austrian newspaper Der Standard last week that Slovakia should not have to support EU efforts to resettle migrants.
"Who bombed Libya?" Fico was quoted as saying; "Who created problems in North Africa? Was it Slovakia? No."
Resource: World Bulletin, August 20 ,2015