In less than two weeks Islamic State group jihadists have claimed four bloody assaults in France and Germany that killed nearly 90 people, wounded hundreds and left the continent on edge.
"It is obvious that potential terrorists could have used uncontrolled migration to smuggle in weapons and explosives," said Fico, whose country currently holds the rotating presidency of the European Union.
"Therefore the possibility of more ... Terrorist attacks is very, very high. There is potential for this," he told reporters in Bratislava.
"During the large influx of migrants, anyone could have come here," he said.
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"What on Earth do these people have in their backpacks? Why don't we take a look? Besides mineral water, food and clothes, there could be something else."
Earlier this year Fico filed a lawsuit against an EU-wide quota plan to redistribute refugees across the bloc after insisting it was committing "ritual suicide" with its acceptance of hundreds of thousands of migrants, mostly refugees from war-torn Syria.
His anti-migrant policies have echoed eastern EU hawks like Czech President Milos Zeman, Hungarian Premier Viktor Orban and Poland's Jaroslaw Kaczynski.