Delivering BBC Radio 4's Thought for the Day, the Prince of Wales said the rise of populist groups "aggressive" to minority faiths had "deeply disturbing echoes of the dark days" of the 1930s.
In the Christmas message, he urged respect for those of different faiths.
He said religious freedom was a "choice between life and death" for some.
It is the third time he has given the address on the Today programme.
The prince said he had recently met a Jesuit priest from Syria who described the plight of Christians he was forced to leave behind in the country.
He said: "He told me of mass kidnappings in parts of Syria and Iraq and how he feared that Christians will be driven en masse out of lands described in the Bible.
"He thought it quite possible there will be no Christians in Iraq within five years.
"Clearly, for such people, religious freedom is a daily, stark choice between life and death."
The prince said the scale of religious persecution around the world was "not widely appreciated" and was not limited to Christians, but included many other minority faiths.
He told listeners he was was born just after the end of World War Two in which his parents' generation had fought against an attempt to "exterminate the Jewish population of Europe."
He went on: "That, nearly seventy years later, we should still be seeing such evil persecution is, to me, beyond all belief.
"We owe it to those who suffered and died so horribly not to repeat the horrors of the past."
Prince Charles urged people to remember the story of the Nativity this Christmas, which was about "the fleeing of the Holy Family to escape violent persecution".
He asked listeners to remember that the Prophet Mohammed migrated from Mecca to Medina because he was "seeking the freedom for himself and his followers to worship".
The Prince said: "Whichever religious path we follow, the destination is the same - to value and respect the other person, accepting their right to live out their peaceful response to the love of God."

As the duo perform live in Stockholm on Saturday night, they will be cheered on by Joe Woolford's friends and family in Ruthin, Denbighshire.
A party has been organised by his uncle where locals can watch the contest on a giant screen.
Geraint Woolford said the town was "buzzing" about the contest.
Joe, 21, will performing You're Not Alone with Jake Shakeshaft, 20, from Stoke-on-Trent in the annual competition.
Both singers were former contestants on The Voice UK.
Joe's family, including his mother Ffion, stepfather Krino Pab, father Alun Jones, sister Misha and younger brother Zac are flying to Sweden to join the 16,000-strong audience watching the final in the city's Globe Arena.
An estimated worldwide TV audience of 200 million viewers is also expected to tune in.
Mr Woolford, a local councillor, said: "We're all very proud of him. Everyone is talking about it... and he's really putting Ruthin on the map internationally.
"A lot of us would have liked to have travelled to Stockholm to be there with him, but it's just too expensive, with ticket prices ranging from Â£350 to Â£2,500.
"But we'll have a real celebration ourselves, especially if Joe and Jake win."
Joe's mother, Ffion Woolford, added: "I've only managed to speak to him for a brief time this week because he's so busy with rehearsals.
"He's incredibly excited and really looking forward to the contest. The arena where he'll be singing is vast, but we're sure we'll do well and I'm looking forward to being there to support him."
Speaking ahead of the event, Joe and Jake said they were quietly confident their song could do well - despite the UK's recent track record.
We've done a lot of preparation, we've been rehearsing non-stop, we've been practising movement, we've been running in and out of the studio," Joe said.
"We want to get a good result for the UK."
The Eurovision final is on BBC One on Saturday 14 May at 20:00 BST.
Prince Charles has spoken out about the danger of religious persecution, warning against a repeat of "the horrors of the past".
[NEXT_CONCEPT]
They may be carrying the UK's hopes of success at Eurovision but Joe and Jake will have strong support from the home town of one of the singers.