The heir to the throne was speaking as a new report suggests Christians in 41 per cent of the world's countries are now suffering because of their faith.
He's recorded a video message saying: "The horrendous and heartbreaking events in Iraq and Syria have brought the subject of religious freedom and persecution to the forefront of the world's news.
"It is an indescribable tragedy that Christianity is now under such threat in the Middle East; an area where Christians have lived for 2,000 years, and across which Islam spread in 700AD, with people of different faiths living together peaceably for centuries."
He also encouraged Muslim leaders to not remain silent over a lack of respect between faiths and to bring about greater interfaith dialogue.
Prince Charles went on to call on Governments to do more to stop the persecution of Christians around the world and to make sure they honour the rights of people to practise their faith.
To watch the whole video message click here.