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| A dinghy carrying Afghan, Syrian and Iranian migrants arrives in the port of the village of Sikaminea on the Greek island of Lesbos on August 20, 2015 |
This would be a two-year process, ministry spokeswoman Michaela Paulenova told AFP, adding that it had decided to accept only Christians because they "have a great potential to seamlessly integrate into our society."
She said Slovakia has few Muslims and no mosques.
"We have nothing against religion, nor is it discrimination. It is just an effort on Slovakia's part to make this integration successful," she said.
"If these people come to Slovakia and subsequently leave our country, then our solidarity would be false and insincere."
However, a UN official called for "an inclusive approach".
"We urge countries not to discriminate," Babar Baloch, the Central European spokesman for the UN refugee agency told AFP.
A barrage of alarming statistics this week showed that hundreds of thousands of migrants -- many fleeing war and persecution in countries like Syria -- are pouring into the 28-member EU, with no end in sight.
EU border agency Frontex on Tuesday reported a record high of 107,500 migrants at EU borders last month.
The EU has approved 2.4 billion euros ($2.6 billion) of funding to help member states cope with the flood of migrants.
Slovakia has granted asylum to 650 people since it split from the Czech Republic in 1993, according to the interior ministry.
An opinion poll released in June showed that 70 percent of Slovakia's 5.4 million citizens do not want to take in refugees or migrants, a sentiment echoed by most EU member states.
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