Meanwhile, the UN says some of the 50,000 members of the Yazidi religious minority trapped by IS on Mount Sinjar have been rescued.
IS controls parts of Iraq and Syria and says it has created an Islamic state.
Nineveh, located 400km (250 miles) north-west of Baghdad, is home to a large number of religious minorities.
Tens of thousands have been forced to flee since the Islamist rebels launched their onslaught in the north in June.
In other developments
- IS said it had captured the strategic Mosul dam on the Tigris river – a claim denied by Kurdish forces who insist they are still in control
- At least six people died when a car bomb exploded near a Shia Muslim mosque in the northern city of Kirkurk
Christian ‘catastrophe’
A majority of Nineveh inhabitants left their homes overnight, according to Fraternite en Irak, an international Christian organisation based in Paris.
As many as 100,000 people are believed to be fleeing toward the autonomous Kurdistan Region.
Kurdish forces, known as the Peshmerga, have been fighting the IS militants’ advance for weeks.
The Peshmerga’s commander in Qaraqosh reportedly told the town’s archbishop late on Wednesday that the forces were abandoning their posts.
Several senior clergymen in Nineveh confirmed the town had fallen.
“It’s a catastrophe, a tragic situation: tens of thousands of terrified people are being displaced as we speak,” said Joseph Thomas, the Chaldean archbishop of the northern city of Kirkuk.
Eyewitnesses in Qaraqosh said IS militants were taking down crosses in churches and burning religious manuscripts.
The town – referred to as Iraq’s Christian capital – is located 30km south-east of the city of Mosul, which was captured by IS in June.
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