In an article he wrote for The Daily Telegraph, Lord Carey said as violent conflict has erupted again in Syria he doubts that Syrian Christians will have much help from the UK government because they are of the "wrong faith".
He referenced how refugees of other faith groups were supposedly favoured over Christians.
"Of the refugees who came here in 2015 under the Vulnerable Persons Scheme, only 1.6 per cent were Christians," he said.
"That's despite this group being 10 per cent of the Syrian population.The situation for Christians seeking asylum has worsened.
"In 2016 only 0.4 per cent were Christians. In 2017, 0.2 per cent. And in the early part of last year none of the 1,112 refugees we took in were Christians. The Yazidi and Druze minorities have been treated just as unfairly."
He added that the government states that their selection of refugees who are allowed to settle in the UK is dependent on their suffering. However, Lord Carey highlighted what deems is an issue in the selection process.
"In their supposed blindness to religion they allowed the process of choosing refugees to be dominated by workers for the UN Refugee Agency (UNHCR) in refugee camps," he said.
"Sunni Muslims – 74 per cent of Syria's population – have made up 99 per cent of the refugees we admit.
"UK officials eventually conceded the obvious: Christian refugees are "reluctant" to enter the camps. It is a reluctance that stems from the fact that they have faced persecution even inside them."
Lord Carey emphasised examples of church bombings and Christian killings in the Middle East as reasons why Christian persecution should be taken seriously.
"This oppression has prompted an extraordinary exodus: Syria's Christian population plunged from 1.7 million in 2011 to just 450,000 last year," he said.
"In neighbouring Iraq, Christians have all but disappeared – down from 1.5 million in 2003 to 120,000."
Lord Carey acknowledged the Foreign Office's move to commission a report by the Bishop of Truro which speaks of Christianity being "wiped-out in parts of the Middle East".
"But this report only addresses the Foreign Office, not the Home Office which has power over the fate of asylum seekers," he said.
"The failings of officials are not isolated aberrations but a window into the soul of our civil service which just as readily discriminates against Christians already here."
He said he hopes that the government will not try to defend "the indefensible" in the judicial review and will instead make changes to its current Syrian refugee settlement program.
The Home Office said in a statement to Premier: "The UK has a proud history of granting asylum to those who need our protection.
"The Vulnerable Persons Resettlement Scheme prioritises the most vulnerable refugees who have fled the Syrian conflict, regardless of race, religion or ethnicity.
"We have worked with the UNHCR and other partners to reach groups that might be reluctant to register for the scheme or may be unaware of the options available to them. These groups include religious minorities in the region."
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