Prince Charles urged religious leaders to encourage followers to respect those of other faiths, drawing on the current persecution of Christians in the Middle East as an example where that respect is lacking.
Charles spoke in a video aired on Tuesday to accompany a report by the Catholic charity Aid to the Church in Need.
"It is an indescribable tragedy that Christianity is now under such threat in the Middle East," he said.
Islamic State fighters drove Christians from Iraq's northern city of Mosul in July, ending a presence stretching back to the early years of Christianity. The Sunni Islamist group has also targeted Shi'ite Muslims and religious minorities, executing hundreds of captives in Iraq and neighbouring Syria.
The Prince said that religious leaders should be vocal and different faith groups should work together.
"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.
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, 88, has never aired personal sentiments.
However, Prince Charles has often courted controversy by voicing strong views on the environment, architecture and social affairs.
He 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" upon taking 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 Aid to the Church In Need report identified 81 countries where religious freedom is impaired or in decline, with 55 countries showing deteriorating conditions for religious freedom between October 2012 and June 2014.