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Fleeing Iraqi citizens from Mosul and other northern towns wait to cross to secure areas at a Kurdish security forces checkpoint in the Khazer area, between the Iraqi city of Mosul and the Kurdish city of Erbil, northern Iraq, on June 25, 2014.HUSSEIN MALLA/The Associated Press

Thousands of Iraqi Christians arrived in Kurdish-controlled areas on Thursday after Islamist militants attacked one of the last Christian enclaves in the country.

A staff member from the International Organization for Migration said that between 2,000 and 3,000 people arrived Wednesday night and Thursday morning at a converted youth centre in Ainkawa, a Christian town on the outskirts of the Kurdish capital of Erbil, that was serving as a temporary refugee-processing hub. Thousands of other Christians were reported to have sought protection with local families in Erbil and other Kurdish cities.

(Learn more about the religious divisions behind the Iraq conflict with Patrick Martin's easy explanation)

The refugees were fleeing an attack by the extremist Islamic State in Iraq and the Levant on Qaraqosh, an historic Christian town outside the city of Mosul. In recent weeks, The Sunni extremist ISIL has made stunning advances in Iraq, seizing the cities of Mosul and Tikrit, as well as border crossings to neighbouring Jordan and Syria, as it pushes towards Baghdad.

ISIL is supported by remnants of the Baath Party of former dictator Saddam Hussein, as well as many local Sunni Muslim tribes opposed to the Shia-dominated government of Prime Minister Nouri al-Maliki.

Qaraqosh residents and Kurdish officials say ISIL attacked Qaraqosh – which had been under the joint protection of Kurdish peshmerga fighters and local Christian militiamen – late Wednesday night. Although the attack was apparently repulsed, several mortar rounds landed in Qaraqosh, a town of 50,000, provoking a mass exodus.

Until Wednesday, Qaraqosh had been seen as a safe haven for Christians fleeing violence and persecution in Mosul and other cities. Many residents had moved there following a wave of murders and threats targeting Mosul's Christians in 2008.

Lebanon's an-Nahar newspaper reported this week that Mosul's remaining Christians had been told by ISIL that they needed to pay a $250 head tax or immediately leave the city.

Iraq's Christian population – one of the oldest in the world – has fallen from 1.5 million before the U.S. invasion in 2003 to an estimated 450,000 today. Many of those who remain now live in the semi-autonomous Kurdish region, the only part of Iraq under secular government. (Though Qaraqosh is outside the area governed by the semi-autonomus Kurdistan Regional Government, peshmerga fighters were invited to help protect the city after ISIL captured Mosul earlier this month.)

Ano Jawhar Abdoka, a representative of the Kurdistan Democratic Party in Ainkawa, said additional peshmerga fighters had been sent to defend Qaraqosh on Thursday. It's not clear how many residents remain in the town.

"Most of Qaraqosh came to Kurdistan because they feel safe here and closer to the Kurdish nation … I hope Iraq will break up and Qaraqosh will become part of [an independent] Kurdistan," said Withaq Shamoun, a 37-year-old labourer who arrived in Ainkawa Thursday morning with his wife and two children. The four were sharing a single mattress as they awaited news about temporary accommodation.

Those escaping Qaraqosh arrive as the Kurdistan Regional Government is already struggling to deal with a mounting refugee crisis. The region – which normally has a population of six million – currently hosts an estimated 500,000 refugees from other parts of Iraq, plus another 250,000 who fled the war in neighbouring Syria.

The rapid advance of ISIL has created fuel shortages in the Kurdish north, with lineups at gas stations stretching hundreds of cars long, and other stations completely out of supply.

"It's very stressful for the region. The Kurdish economy and resources are being strained," said Jeffrey Bates, a spokesman for UNICEF Iraq. He said that while numbers were changing by the hour, half of all refugees in the Kurdish areas are believed to be under the age of 17, while 20 per cent are under 5 years old.

Mr. Bates said donor fatigue – and specific qualms about sending money to Iraq – meant that aid agencies were struggling to cope with the rapidly evolving crisis. "There's money coming in, there's support coming in, but it's not enough."