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Islamic State militants are behind Europe's snowballing refugee crisis and are the top danger facing the region, the Czech Republic's finance minister told CNBC on Friday.

"I think Islamic State is the biggest danger for us—and these people are leaving their countries because of Islamic State," Andrej Babis told CNBC, as European finance ministers met in Luxembourg on Friday.

Babis' comments came as thousands of migrants and refugees converge on Southern and Eastern Europe, mainly from war-torn Syria, but also from other countries in the Middle East and Africa. Many of these people are trying to travel north across the continent to reach prosperous Northern European countries such as Germany that are viewed as sympathetic to their plight.

Babis said that support from the international North Atlantic Treaty Organization (NATO) was needed to help secure Europe's borders and combat the traffickers smuggling people into the region.

Migrants walk along a rail track in the rain from Roszke to Szeged in Hungary, September 10, 2015.
Laszlo Balogh | Reuters

"The European members of NATO and armies of Europe have to join forces," he told CNBC.

The president of the European Commission, Jean-Claude Juncker, has called on European countries to take "concerted action" to deal with the crisis. His suggestions include a compulsory quota system across Europe to ensure that all countries take in a certain number of displaced people.

However, there is strong opposition to the mandatory relocation of migrants, particularly in Eastern Europe, with the Czech Republic and Slovakia criticizing the proposals. Poland and Romania are also opposed to taking in more migrants, although the former, like the Czech Republic, has reluctantly agreed to do so.

Speaking to CNBC in Luxembourg on Friday, Babis said it was important for a system to be in place to process asylum claims.

"We have to separate the humanitarian refugees from the economic ones," he said. "For the Czech Republic, who can count all these people? We need to have a system," he told CNBC.

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In the meantime, Babis proposed closing the Schengen Area, a free-movement zone comprising of 26 European countries that have abolished the need for passports and other types of control at their common borders.

"We have maybe to learn about the immigration policy that was done in the United States—remember Ellis Island—Canada and Australia and we have to really close the Schengen border," he told CNBC on Friday.

"We have, really, to maybe organize immigration camps under the supervision of (the) United Nations and we have to fight against the smugglers, because this is the problem, they decide today which immigrants are coming to Europe."

Also this week, Babis' counterpart from Luxembourg told CNBC that the migration and refugee crisis would not go away any time soon.

"The refugee crisis is obviously a big subject and the problem is there to stay. It's not going to be solved in a short-term manner because as long as we have war in the Gulf area in the Middle East and northern Africa, there is going to be refugees," Luxembourg Finance Minister Pierre Gramegna told CNBC Thursday.

Migrants storm into a train at the Keleti station in Budapest, Hungary, September 3, 2015, after Hungarian police withdrew from the gates.
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The authorities appear to be struggling to cope with the influx, with scuffles breaking out between large groups of migrants on the move and police in Greece, Macedonia and Hungary. On Wednesday, Danish police closed a motorway and rail links with Germany in a bid to stem the procession of migrants heading northward to Sweden.

Juncker's proposed quota system would relocate up to 160,000 migrants but that could prove far from adequate, as the United Nations' refugee agency has forecast that at least 850,000 people will cross the Mediterranean seeking refuge in Europe this year and next.

Furthermore, the process of relocating refugees—or repatriating those whose asylum claims are turned down—is easier said than done.

Any move to force countries to accept would be controversial and even Germany, which has called on Europe to "pull its weight" in the crisis, said the quota system would only be one step to resolving it.

Tents are seen at a refugee camp on the outskirts of Mytilini on September 8, 2015 in Lesbos, Greece. More than 230,000 people have landed on Greek shores this year.
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Hoping to cross into Hungary, migrants walk along a railway track outside the village of Horgos in Serbia, towards the border it shares with Hungary, September 2, 2015.
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Police stand guard as migrants sit on the platform of Keleti station after it was reopened this morning in central Budapest on September 3, 2015.
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Syrian refugees and other migrants are stopped by Macedonian police at the Greek-Macedonian border, near the village of Idomeni, Aug. 22, 2015.
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Luxembourg's Gramegna was in favor of Juncker's plan, although he conceded the challenges posed by mass migration, ranging from language and skills acquisition to the broader cultural impact.

"Juncker announced a plan for a considerable number of refugees and I know there are a number of countries that have a problem with this, but we have to recognize that Europe has always been…a safe haven for refugees," he told CNBC.

Gramegna added that it was unlikely that financial penalties would be meted out to countries that didn't play a role in relocation.

"This is an issue that has been raised, but in Europe, we have the habit of negotiating and finding compromise so I'm pretty confident we can sit around the table and find the right arguments without punishments having to be used," he concluded.

Reporting by Julia Chatterley, writing by Holly Ellyatt.