Pope Francis takes three families of Syrian refugees on plane back to Rome from Greek island of Lesbos

The Vatican said 12 people, including six children, were taken as 'a gesture of welcome'

Three families of Syrian refugees have been taken to Rome with the Pope after he offered them a place on his plane.

They were among thousands of people trapped on the Greek island of Lesbos following the controversial EU-Turkey deal, under which all asylum seekers arriving over the Aegean are detained as they await their fate.

Syrian refugees board the Pope's plane in Lesbos yesterday (AFP/Getty Images)

A statement from the Vatican said 12 people, including six children, were taken as part of a “gesture of welcome regarding refugees” during Pope Francis' tour of the island on Saturday.

Their homes had been bombed during the Syrian civil war: two families came from Damascus and others escaped Isis territory in Deir ez-Zor.

Footage showed them lined up on the tarmac of Lesbos’s main airport as Pope Francis said his farewells to Catholic and Orthodox leaders who accompanied him on Saturday’s tour of the island.

One woman, wearing Western clothing, was unable to contain her grin as she stood next to her husband, carrying their sleeping son.

Next to them, another mother wearing a headscarf played with her daughter’s hair while her husband and teenage sons watched the preparations to the waiting plane excitedly.

In the third family, a father held his young children’s hands as they were fussed by relatives.

Pope Francis greets migrants at Moria detention centre on Lesbos (Reuters)

Their unexpected flight to Europe is a provocative move for the pontiff, coming amid continued protests over measures seeing all asylum seekers arriving clandestinely over the Aegean detained.

The Syrians taken back to Rome all arrived before the 20 March deadline, meaning they are not subject to the new rules.

The Vatican said it will take responsibility for supporting the families, who will initially be settled by the Catholic Sant'Egidio community.

“The Pope’s initiative was brought to fruition through negotiations carried out by the Secretariat of State with the competent Greek and Italian authorities,” a spokesperson added.

“All the members of the three families are Muslims. Two families come from Damascus, and one from Deir ez-Zor, in an area occupied by Isis. Their homes had been bombed.”

Pope Francis had visited the Moria detention centre, where almost 3,000 people are being held in conditions described as “appalling” by charities.

He also visited the island’s capital of Mytilene for a prayer service to commemorate the hundreds of migrants who have died attempting to reach Europe’s shores.

In a speech, he told refugees they were “not alone” and urged them not to lose hope.

“We have come to call the attention of the world to this grave humanitarian crisis and to plead for its resolution,” he added.

“We hope that the world will heed these scenes of tragic and indeed desperate need, and respond in a way worthy of our common humanity.”

The Vatican said the five-hour visit to Lesbos was purely humanitarian and religious in nature, not political, but the Pope’s message to Europe was clear.

Appearing to refer to border closures and fences erected across the continent during the refugee crisis, he said the world needs bridges, not walls.

Pope Francis greets migrants and refugees at the Moria refugee camp on the Greek island of Lesbos, April 16, 2016. (Reuters)

“Barriers create divisions instead of promoting the true progress of peoples, and divisions sooner or later lead to confrontations,” he added.

Controversy continues over the situation in Lesbos, which is now subject to the 18 March EU-Turkey deal.

It stipulates that anyone arriving clandestinely on Greek islands will be returned to Turkey unless they successfully apply for asylum in the country.

For every Syrian sent back, the EU will take another Syrian directly from Turkey for resettlement in Europe but other nationalities make up more than half of those arriving.

In return, Turkey was granted concessions including billions of euros to deal with the more than 2.7 million Syrian refugees living there, and a speeding up of its stalled accession talks with the EU.

Despite the measures, condemned by human rights groups as “shameful” and “inhumane”, desperate asylum seekers fleeing war and persecution in the Middle East and Africa continue to arrive.

Frontex, the European border agency, intercepted a dinghy carrying 41 Syrians and Iraqis off the coast of Lesbos, three hours before the Pope’s arrival.