The Aid to the Church in Need document says if the exodus of faithful from Iraq continues at existing levels the religion will be wiped out in the country by 2020.
Christians in Syria number as few as 500,000 today compared to 1.25 million in 2011, the report says.
Prime Minister David Cameron has given his backing to the report, which is called Persecuted and Forgotten.
David Cameron said: "Every day in countries across the world, Christians are systematically discriminated against, exploited and even driven from their homes because of their faith.
"This [Persecuted and Forgotten] report serves as a voice for the voiceless, from their prison cells, and the places far from home where they have sought refuge."
The First Minister of Scotland, Nicola Sturgeon, also sent a message of support for the charity's report.
She said: "Only by publishing reports such as this and identifying the extent and scale of the problem can we hope to take steps to address the persecution of minorities that sadly still exists across the world."
Elsewhere the Pope said the report was "deeply appreciated" and showed the "plight and suffering of Christians persecuted for their faith".
The report outlines the "religiously motivated ethnic cleansing" of Christians by Islamist terror groups especially in Iraq and Syria but also in parts of Africa.
Since 2013 the situation for Christians has worsened in 15 of the 19 core countries under review, it said.
In 10 countries - more than half - the persecution is ranked "extreme" - up four from the last edition of Persecuted and Forgotten report which covered 2011-13.
The greatest threat to Christinaity was claimed to be Islamism but growing problems caused by other extremist religious groups - militant forms of Hinduism, Judaism and Buddhism - are also highlighted.
Persecuted and Forgotten editor John Pontifex said the report was a "shocking read for shocking times".
He added: "A cultural genocide of Christians is erasing the presence of faithful from large swathes of the Middle East, the very heartland of the Church.
"Far from laying the entire blame for persecution against Christians at the door of extremist Islam, Persecuted and Forgotten demonstrates that many of the problems stem from non-Muslim extremist - nationalist - faith groups and historically communist totalitarian regimes."
