Prince Charles was speaking at an Advent reception hosted by the Archbishop of Westminster, Cardinal Vincent Nichols.
He met members of the Middle Eastern Christian community and heard their stories about how Islamic extremism has forced them to flee.
He said: "The greatest challenge we face is how to ensure that the spiritual and cultural heritage of Christianity in the middle east is reserved for future generations.
"Quite apart from doing all we can to provide practical support to those who are persecuted."
He issued a dire warning about the future of Christians living in Iraq saying they will "disappear" within five years.
The heir to the thrown said that "emergency help" at an international level was needed to avert the disaster.
He said: "Their suffering is symptomatic of a very real crisis which threatens the very existence of Christianity in the land of its birth.
"In fact according to Aid to the Church in Need, which is a truly remarkable organisation, Christianity is on course to disappear from Iraq within five years unless emergency help is provided on a greatly increased scale at an international level.
"This affects us all, consequently the greatest challenge we face is how to ensure the spiritual and cultural heritage of Christianity in the Middle East is preserved for future generations."
He added: "At this traditional time of prayer and reflection on the mystery of the Incarnation, it seems to me vital that we pause for more than a moment to think about the plight of Christians in the lands where the Word was actually "made flesh and dwelt among us".
"For, despite what the brainwashed militants would have people believe, Christianity is not a "foreign" religion.
"It is, perhaps, worth remembering that those of us who are members of the Church of England will be only too familiar with the Nicene Creed, whose words were first formulated in the Middle East in the fourth century.
"Far from Christianity being a "Western" religion, Christianity was born in and shaped by the East.
"This is what makes the plight of our fellow brothers and sisters in Christ so especially heart-breaking."