In a video for the religious freedom charity Aid to the Church in Need, Charles said the scale of the problem is under-estimated and not simply limited to Christians in the Middle East, claiming research shows other groups including Jews and Yazidis are also being targeted.
He said: "We are now seeing the rise of many populist groups across the world that are increasingly aggressive towards those who adhere to a minority faith.
"All of this has deeply disturbing echoes of the dark days of the 1930s.
His Royal Highness went on to say it was "beyond all belief" to him "such evil persecution" still exists, more than 70 years after the Second World War.
He added: "I was born in 1948, just after the end of World War Two, in which my parents' generation had fought and died in a battle against intolerance, monstrous extremism and an inhuman attempt to exterminate the Jewish population of Europe."
Charles also described a recent meeting with a Jesuit priest from Syria who feared there may not be a single Christian left in Iraq within five years.