The Pope has warned the refugee crisis in Europe could see terrorists infiltrating the continent's shores, in an apparent reference to Islamic State extremists.

Despite conceding that the influx of migrants and refugees could pose a security threat in today's world, Pope Francis recalled that the Bible requires that strangers be welcomed.

"It's true that 400 kilometres from Sicily, there is an exceedingly cruel terrorist guerrilla group, and it's true there's the danger of infiltration," he told Portuguese Catholic radio station Radio Renascenca.

The pontiff also blamed the mass influx of migrants from Syria and the surrounding areas on an "unjust" global economic system forcing hundreds of thousands of people to flee war and poverty in search of better lives.

Pope Francis repeated his call for parishes around the world to welcome in a migrant family, and said two refugee families have been identified to move into Vatican housing. They can stay "as long as the Lord wants," he said.

He applauded those European countries that had welcomed in migrants and warned what awaits those that don't: "On Judgment Day, we already know what we'll be judged on," he said, reciting the Biblical verse from Matthew 25: "When I was hungry, did you give me food?"

Those countries that answered "Yes" - "I congratulate them. They'll pass the test," he said.