Iraq's Christians are in their 'darkest hour' as they face choice of converting or leaving

An Iraqi nun, left, speaks with a Christian man who fled with his family from Christian villages near Mosul province in Iraq, at a school which turned as a shelter for the displaced Christian families, in Ainkawa, a suburb of Irbil, with a majority Christian population, Iraq, Friday, June 27, 2014.(AP)

Christians in Iraq are continuing to leave their homes in large numbers following the ISIS takeover but those unable to leave are facing brutality and hardship under the militants, Barnabas Fund is warning.

Those still in the areas taken over by ISIS are being told to pay a $250 tax for being non-Muslims, but many of them cannot afford to pay it.

There were harrowing reports in the last week of a man being forced to watch ISIS militants rape his wife and daughter after the family was unable to pay the tax.

Last weekend, two nuns, Miskintah and Utoor Joseph, and three young Christians, Hala Salim, Sarah Khosaba and Aram Sabah went missing on their way back to Mosul after taking orphaned girls to Dohuk for their safety. It is feared they have been abducted by militants.

"Christians in Islamic State territory are clearly in extreme danger," said Barnabas Fund.

The organisation is providing aid to many of the Christians who have fled their homes since ISIS took over and started implementing strict Sharia law.

Last week, UNHCR said 10,000 people had fled from Christian communities in Qaraqosh, near Mosul, with many of them ending up in Erbil with very few possessions.

It said some 300,000 Iraqis had arrived in the Kurdistan region from Mosul's Ninewa province.

Dr Patrick Sookhdeo, International Director of Barnabas Fund, said: ""This is one of the darkest hours ever for Christians in Iraq. Our brothers and sisters are being repeatedly uprooted as the jihadists advance, imposing their brutal version of Islam.

"For those who cannot escape for whatever reason, the situation is even more dire. Please continue to help us meet the needs of Christians who are caught up in this escalating crisis."