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Refugees and migrants rest after their arrival at the Greek island of Lesbos after crossing the Aegean sea from Turkey on October 5, 2015. Europe is grappling with its biggest migration challenge since World War II, with the main surge coming from civil war-torn Syria.ARIS MESSINIS/AFP / Getty Images

The Prime Minister's Office directed Canadian immigration officials to stop processing one of the most vulnerable classes of Syrian refugees this spring and declared that all UN-referred refugees would require approval from the Prime Minister, a decision that halted a critical aspect of Canada's response to a global crisis.

The Globe and Mail has learned that the Prime Minister intervened in a file normally handled by the Citizenship and Immigration department in the months before dramatic images of a dead toddler brought the refugee crisis to the fore. The processing stop, which was not disclosed to the public, was in place for at least several weeks. It is unclear when it was lifted. At the same time, an audit was ordered of all Syrian refugees referred by the United Nations in 2014 and 2015.

(Four things to know: See how the major parties propose to help Syrian refugees)

The Prime Minister's Office asked Citizenship and Immigration for the files of some Syrian refugees so they could be vetted by the PMO – potentially placing political staff with little training in refugee matters in the middle of an already complex process.

PMO staff could have also had access to files that are considered protected, because they contain personal information, including a refugee's health history and narrative of escape, raising questions about the privacy and security of that information and the basis on which it was being reviewed.

As a result of the halt, and the additional layers of scrutiny, families that had fled Syria and were judged by the United Nations refugee agency to be in need of resettlement had to wait longer to find refuge in Canada. It also meant there were fewer cases of UN-referred Syrians approved and ready for sponsorship when the public came forward in large numbers after the drowning death of three-year-old Alan Kurdi in August.

The Prime Minister's Office did not directly respond to a request for comment, nor did it confirm Stephen Harper's involvement.

A spokesman for Citizenship and Immigration Minister Chris Alexander, however, said the government was concerned about the integrity of the system and ensuring that security was not compromised in any way.

"The processing of Syrian Government Assisted Refugees resumed only after there was confidence that our procedures were adequate to identify those vulnerable persons in most need of protection while screening out threats to Canada," said Chris Day, spokesman for Mr. Alexander. He noted that processing of privately sponsored refugees, who are not referred by the UN but by their Canadian sponsors and who make up a growing portion of Canada's refugees, continued throughout this period.

Critics have long complained about the centralization of decision-making in the PMO – and it would be unusual for a prime minister to sign off on refugee files that have already been vetted by the UN refugee agency, Canadian visa officials and in a small minority of cases by the Canadian Security Intelligence Service and the Canada Border Services Agency.

The opposition parties and refugee advocates have accused the government of being slow to act in the face of the world's largest refugee crisis in decades. Two weeks ago, the United Nations High Commissioner for Refugees called on Canada to do more to aid in the emergency, citing the risk of food shortages and a deterioration in living conditions for Syrian refugees.

More than 2,000 Syrian refugees have died trying to flee the region and half a million have arrived in Europe this year. The Conservatives have pledged to speed up processing to welcome 10,000 refugees by September, 2016, and during the campaign promised to take an additional 10,000 "from the region" if re-elected.

One of the government's concerns that led to this spring's processing halt centred on the hiring of a foreign NGO to screen refugees referred by the UNHCR. The Danish Refugee Council was hired to assist with the processing of refugees from the Syrian crisis. The contract terms have not been disclosed publicly but the council confirms it is working in partnership with Canada. It referred questions to the Canadian government. Why Canada hired a foreign NGO and at what cost is not clear.

Normally, Canada gets its government-assisted refugees referred by the UNHCR, which does its own assessment of the candidates for resettlement before Canada interviews them again, goes through security checks and orders health exams. They are usually among the most vulnerable of all refugees, since the UNHCR can offer resettlement in the West to only about 1 per cent of those displaced around the world. (Privately sponsored refugees can be selected regardless of relative need by family and faith groups in Canada.) Private groups can also sponsor UN-referred refugees as Blended Visa Office Referred cases.

The shutdown in processing potentially threatened Canada's ability to meet its refugee resettlement targets for this year, although after the outcry stirred by photographs of Alan Kurdi's body washed up on the shore, the government has provided more resources to process applications.

The department of Citizenship and Immigration said Canada issued visas to only 308 UN-referred refugees from Syria through the first eight months of this year, compared with 1,513 privately sponsored refugees.

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