A group of Syrian refugees arrive to board a plane to travel to Italy with Pope Francis

Pope Francis has taken a dozen highly vulnerable refugees who faced deportation from the Greek island of Lesbos back to Rome, offering them refuge in a rebuke to the EU’s policy of sending migrants and refugees back to Turkey.

The leader of the Roman Catholic church made the unprecedented intervention on Saturday during a trip to the island to highlight the refugee crisis unfolding across the continent.

The pontiff spent five hours on Lesbos with Bartholomew I, the spiritual leader of the world’s Orthodox Christians, and Ieronymos II, the archbishop of Athens and Greece, meeting refugees and holding a service to bless those who have died trying to reach Europe.

Fuelling belief that the Catholic church is at odds with the EU’s stance on the crisis, Pope Francis took 12 refugees back to the Vatican. An official confirmed all those taken from the camp were Syrian Muslims, six of them minors who arrived Lesbos before the deportation deal came into effect.

 A group of Syrian refugees arrive to board a plane to travel to Italy with Pope Francis

A spokesman for 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.

“Two families come from Damascus, and one from Deir Azzor (in the area occupied by Isis). Their homes had been bombed. The Vatican will take responsibility for bringing in and maintaining the three families. The initial hospitality will be taken care of by the Community of Sant’Egidio.”

The pontiff spent the morning meeting hundreds of migrants and refugees in a notorious detention centre on the island. Men and women held in the camp wept as he toured the site.

A woman kisses the hand of Pope Francis as he greets people at the Moria refugee camp. Photograph: Filippo Monteforte/AFP/Getty Images

The pope was met at Mytilene’s airport by the Greek prime minister, Alexis Tsipras, at the start of his biggest effort yet to highlight the humanitarian crisis unfolding in Europe. Lesbos has borne the brunt of the refugee influx with more than 850,000 of the 1.1 million Syrians, Afghans and Iraqis who streamed into Europe last year coming through the island. “Greece has been an example of humanity,” he said.

 

The visit is also seen as a further warming of ties between the western and eastern branches of Christianity, almost a millennium after their bitter split in 1054. In a break with protocol, the pope chose to be driven to the detention camp, in the hills above Mytilene outside the village of Moria, with Bartholomew.

Addressing refugees, he said: “I am here to tell you, you are not alone … The Greek people have generously responded to your needs despite their own difficulties. Yes, so much more needs to be done but let us thank God that in our suffering he never leaves us alone.

“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.”

After having lunch with eight refugees in Moria, the three church leaders held a memorial for the victims of migration at Mytilene’s port – earlier this month the site of the first deportations under the EU-Turkey deal.

Addressing a large crowd, the pontiff issued an appeal for “responsibility and solidarity” towards refugees from the picturesque harbour. He said refugees were forced to live in “a climate of angst and fear and uncertainty over their future”, adding: “Before they are numbers, refugees are first and foremost human beings.”

Greece’s leftist-led government described Saturday’s visit of religious leaders as extremely significant. Tsipras was expected to underline Greece’s increasingly fragile situation in talks with the pope.

 

The country has been struggling to house refugees in makeshift facilities even though the number of arrivals has dropped dramatically since the deportation deal came into effect on 20 March.

For detainees who have arrived since then, conditions have deteriorated dramatically. Human rights organisations have withdrawn from Moria and other detention centres for fear of being associated with an operation of mass expulsions.

On Friday, just hours before Francis’ scheduled visit, detainees in the Lesbos camp chanted “freedom, freedom” as demonstrators denounced their incarceration.

Standing under the razor wire-topped fence, Sham Jutt, a young Pakistani, spoke of the refugees’ plight, saying he hoped the pope could intervene. “We expected a life of hope and now he is our only hope,” said the 21-year-old, adding that he had seen the camp change from being a registration centre to a prison following the controversial pact the EU signed with Turkey.

Before the church leaders’ visit, authorities had gone out of their way to clean up the camp, whitewashing graffiti-splattered walls, replacing tents with containers, installing air conditioning and taking families out of the overcrowded facility to an open-air holding centre nearby.

“In every sense of the word, they have given it a whitewash,” said Jakob Mamzzak, a volunteer from California. “Today we even heard they had given -detainees]-clean clothes-, let them have their first shower in 25 days and brought them good food when the truth is conditions are inhumane.”

Lesbos’s refugee solidarity movement was hoping the pope could bring international attention to the problem. “Since this crisis began we have acted in solidarity with refugees,” said Nikos Zartamopoulos who, with others in the communist-aligned Pame trade union, had demonstrated outside the camp. “We are not against the pope per se. If he can speak out, if he can highlight their plight so much the better.”

The trip came as the head of the Catholic church in England and Wales said the UK’s refugee resettlement programme set up by David Cameron was a “great disappointment”.

Cardinal Vincent Nichols said Britain’s response to the crisis was “going very slowly” and called for a major increase in the number of people being taken in. Asked if he believed governments needed to show more humanity, the archbishop of Westminster replied: “I do.”

He told BBC Radio 4’s Today programme: “I think we have the resources as a very rich country. Think of a country like the Lebanon and some of the other Middle Eastern countries where they have a proportion of refugees present which represents 30-40% of the population and they cope.

 

 “We are a very rich country and I think with a greater cohesiveness between a spirit of willingness that is there among many and mechanisms which governments can put into place, we could be doing more.

“There are aspects of the government policy that are commendable but I’ve said surely that can be speeded up. Surely in the first year we can see really how many could be taken and then multiply that by five. At the moment it’s going very slowly and it’s a great disappointment.”

David Cameron announced plans to resettle 20,000 Syrian refugees in Britain at the height of the crisis. The scheme will cost more than £500m, the government said earlier this week.

Nichols dismissed suggestions that the UK should not be taking in refugees because some Britons are struggling to make ends meet.

“I don’t think the struggle of people in the destroyed villages in and around Mosul and other parts of Syria, those struggles are not the same as our struggles,” he said.

“They are people like ourselves and they are desperate and we should open our hearts as well as our political and financial resources.”