Twelve Syrian refugees were accompanying Pope Francis on his return flight to Rome after his visit to Lesbos on Saturday and will be housed in the Vatican, the Holy See said.

"The pope has desired to make a gesture of welcome regarding refugees, accompanying on his plane to Rome three families of refugees from Syria, 12 people in all, including six children," a Vatican statement said.

The families, all Muslims, had been in Lesbos before the March 20 EU-Turkey deal for returning migrants denied asylum, it said.