The Pope is reportedly planning to take 12 refugees back to the Vatican as he urges Europe to relocate the thousands of asylum seekers trapped in Greece.

A local official confirmed the plan to the AFP news agency as Pope Francis started his tour of the Greek island of Lesbos with Catholic and Orthodox Church leaders.

His plan is not thought to violate the terms of the controversial EU-Turkey deal as the migrants chosen arrived before the deadline of 20 March.

Pope Francis, greeted by Archbishop Ieronimo, arrives on the Greek island of Lesbos on 16 April 2016 (Reuters)

Greece's national broadcaster reported that eight Syrians and two Afghans would be taken on the Pope's plane when he departed Lesbos, but a Vatican official later put the number at 12.

While Syrians have been prioritised by relocation schemes across Europe, Afghans have been excluded from most programmes and barred from crossing borders as they are not automatically considered refugees, despite making up around a quarter of those arriving on the continent's shores.

Pope Francis is expected to call on European countries to relocate thousands of refugees trapped in Greece by shut borders across the continent.

The Vatican previously said the five-hour visit to Lesbos was purely humanitarian and religious in nature, not political, and wasn't meant as a criticism of the deportation programme seeing some asylum seekers sent back to Turkey.

Pope Francis said he intended “to express closeness and solidarity both to the refugees and to the Lesbos citizens and all the Greek people who are so generous in welcoming (refugees).”

Amid deportations, refugees scramble to reach Europe

“Refugees are not numbers, they are people who have faces, names, stories, and need to be treated as such,” a tweet from his official account said as the visit began.

The pontiff has been outspoken in calls for greater compassion and international co-operation in the refugee crisis, denouncing the “globalisation of indifference” during a trip to Lampedusa – another migrant hotspot.

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.

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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 was due to arrive.

He landed at the island’s airport at around 10am local time (8am BST), being greeted on a red carpet by the Greek Prime Minister, Alexis Tsipras, and a delegation of Catholic and Orthodox Church leaders.

The pontiff was due to visit Moria, a refugee camp-turned detention centre currently housing almost 3,000 migrants.