Vatican City (AFP) - Pope Francis on Monday urged European governments to keep welcoming migrants while acknowledging security and other concerns over the recent mass influx of people mainly from the Middle East, Asia and Africa.

Addressing ambassadors to the Holy See in the aftermath of the New Year's Eve mass assaults in Germany's Cologne, the pontiff said the present wave of migration seemed to be undermining the foundations of Europe's "humanistic spirit".

He urged European leaders not to to lose "the values and principles of humanity ... however much they may prove, in some moments of history, a burden difficult to bear."

Francis said Europe was struggling to cope with the unprecedented wave of refugees, which saw over a million people arrive on the continent's shores in the course of 2015.

"Many migrants from Asia and Africa see in Europe a beacon for principles such as equality before the law and for values inherent in human nature," he said.

"All the same, the massive number of arrivals on the shores of Europe appear to be overburdening the system of reception painstakingly built on the ashes of the Second World War, a system that is still an acknowledged beacon of humanity."

He said the sheer size of the influx was causing "inevitable problems" and raising concerns about "changes in the cultural and social structures" of host countries.

"Equally significant are fears about security, further exacerbated by the growing threat of international terrorism," the pontiff added.

The migration crisis -- Europe's worst since World War II -- has caused deep rifts between EU member states and left the bloc's Schengen system of open borders on the brink of collapse.

And the shock generated by events in Cologne at New Year has piled pressure on Chancellor Angela Merkel over her liberal stance towards refugees.

Pope Francis said EU governments could welcome people fleeing conflict, repression and hunger whilst also ensuring the security of their own citizens.

"Europe, aided by its great cultural and religious heritage, has the means to defend the centrality of the human person and to find the right balance between its twofold moral responsibility to protect the rights of its citizens and to ensure assistance and acceptance to migrants," he said.