UN officials say an estimated 200,000 new refugees are seeking sanctuary in the Kurdish north from Islamic extremists

Iraq's largest Christian city was all but abandoned on Thursday as the jihadist advance through minority communities in the country's north-west rampaged towards the Kurdish stronghold of Erbil.

UN officials said an estimated 200,000 new refugees were seeking sanctuary in the Kurdish north from Islamic extremists who had pursued them since the weekend. The city of Qaraqosh, south-east of Mosul, home to around 50,000 Christians was the latest to fall, with most residents fleeing before dawn as convoys of extremists drew near.

Other Christian towns near Mosul, including Tel Askof, Tel Keif and Qaramless have also largely been emptied. Those who remained behind have reportedly been given the same stark choice given to other minorities, including Yazidis: flee, convert to Islam, or be killed.

Christians, Yazidis and Turkmen have been at the frontlines of Iraq's war with the Islamic State (Isis) ever since the jihadist group stormed into Mosul and Tikrit in mid-June. The Iraqi army capitulated within hours, with at least 60,000 officers and soldiers fleeing on the first day of the assault alone.

Ever since, the jihadists have continued to make advances, while Iraqi troops have concentrated on defending Baghdad and the Shia south, leaving the defence of minorities in the north to the Kurdish peshmurga.

However, even the much vaunted Kurdish forces were no match for the heavy weapons wielded by the jihadists as they advanced in recent days. Peshmurga officers ordered troops to withdraw to areas administered by the Kurdish regional government – a clear sign of priorities and of where the battle lines are being drawn.

Without any protection, Yazidis, Christians and Turkmen are being uprooted from communities they have lived in for millennia and the geo-social fabric of Iraq is being rapidly shredded.

While those who have managed to flee the Christian areas have so far had a relatively safe passage to Erbil, tens of thousands of Yazidis remain besieged on a mountain top near Sinjar, with little food or water.

The UN said on Thursday it was able to get some supplies overland to the stranded hordes – avoiding Isis fighters who have surrounded most of Mount Sinjar. Turkish foreign minister Ahmet Davutoglu announced that Turkish helicopters had dropped food and water on the mountain top. Iraqi helicopters have also made food drops, but stranded Yazidis say they do not have enough to survive.

The Chaldean archbishop of Kirkuk, Joseph Thomas, described the situation in northern Iraq as "catastrophic, a crisis beyond imagination". He demanded urgent intervention to save what remained of the area's Christian heritage.

Kurdish officials on Thursday demanded more help in catering for refugees. The Kurdish administered areas have seen staggering numbers cross their notional border since the original Isis onslaught two months ago. In the first week alone, some 500,000 people are thought to have fled towards Erbil.

The capital of the Kurdish north is already home to a new Chaldean Christian community, which fled Baghdad in the wake of an Isis-led massacre inside a cathedral in October 2010. Many fleeing Christians have headed for the Ainkawa neighbourhood, which is home to Baghdad's Christian exiles.

The past 11 years of war and insurrection since the US invasion have led to most of Iraq's Christians fleeing. Numbers have plummeted starkly from an estimated 1 million before 2003 to around 150,000 now. A large number of those who remain are now displaced.

Miriam Dagher, 53, from Qaraqosh, said churches in the city had already been torched and religious insignia smashed. "We stayed as long as we could," she said. "But nothing could save us. This is the end of our community."

Isis has threatened to redraw the unitary borders that were carved out of the ruins of the Ottoman empire. The group's rampant insurgency and the inability of state actors to stop it has rendered the frontier between Iraq and Syria evermore irrelevant.

In the absence of central government authority, Shia militias are taking dominant roles, amplifying sectarian enmity between Islam's two most dominant sects.

Iraq's beleaguered prime minister, Nour al-Maliki, no longer has the authority to unite the country's disparate sects. Maliki, a Shia Muslim, had disenfranchised much of the country's Sunni community over the past three years, some of whom have turned to Isis as a means of reasserting themselves.

After digging in for the past two months, Maliki now faces a desperate battle to form a government, with his key backer Iran understood to have told him that it no longer supports his bid to lead the country for a third term.

Kurdish leader, Massoud Barazani, has said he is moving towards holding a referendum that could pave the way for an independence bid, a move that could spell the end of Iraq, and unsettle surrounding countries, including Syria, Turkey and Iran.