Prince Charles stated it is unjust that Christians experience such violence in a region they have inhabited for 2,000 years, especially considering Islam only spread to the region in 700 A.D.
While the Middle East has experienced numerous conflicts, Prince Charles stated that Christians have co-existed with people of different faiths, living together peacefully for centuries, up until now.
"It seems to me that our future of free society both here, in Britain, and throughout the world, depends on recognizing the crucial role played by people of faith, and of course religious faith is all the more convincing to those outside the faith, when it is expressed with humility and compassion, giving space to others whatever their beliefs," the prince said.
Traditionally, Britain's royal family does not voice political views in public, with the head of state merely a constitutional figurehead. During her long reign, Queen Elizabeth II, 88, has never aired personal sentiments.
Charles sent his prayers to any Christians, Jews, Muslims, Buddhists or Hindus who are facing persecution in the East. He went on to state that if no tolerance or respect exists between world religions, the freedoms of society becomes threatened.
"Rather than remaining silent, faith leaders have, it seems to me, a responsibility to ensure that people within their own tradition respect people from other faith traditions," he said. "We have yet to see the full potential of faith communities working together, however to do this effectively with a truly fraternal approach, requires not only maturity in one's own faith, but also an essential humility."
Charles said his Christian faith has enabled him to speak and listen to people from other traditions, including Islam.
The future king, who will inherit the title "Defender of the Faith" once he eventually takes the throne, also called on governments to uphold article 18 of the Universal Declaration of Human Rights, the freedom to change one's religion or belief.
The video address accompanies the Aid to the Church In Need report, which identified 81 countries where religious freedom is under threat, with 55 countries showing deteriorating conditions for religious freedom between October 2012 and June 2014.
Reuters contributed to this report.