In a lecture on relations between Islam and the West, delivered at Egypt's Al-Azhar University on Tuesday, Charles told an audience of about 800: "The true mark of a civilised society is the respect it pays to minorities and to strangers."
Referring to the cartoons, first published in Denmark, that provoked riots in many Muslim countries for their negative depictions of the Prophet, Charles said: "The recent ghastly strife and anger over the Danish cartoons shows the danger that comes of our failure to listen and to respect what is precious and sacred to others.
"Responsible men and women must work to restore mutual respect between faiths," the prince said in a speech that quoted Jewish, Christian and Muslim scripture.
Charles said: "Highest among those values of our common inheritance, and born of our love of God, must always come respect for each other, and for His creation."
The prince and his wife Camilla, the Duchess of Cornwall, were visiting Al-Azhar, the most renowned Islamic learning institution in the Sunni Muslim world, on the second day of their five-day stay in Egypt.
Britain's Prince Charles delivers
a lecture at Egypt's Al-Azhar
Mohammed Sayed Tantawi, the government-appointed shaikh of Al-Azhar, hosted the couple and awarded the prince an honorary doctorate in recognition of his work in promoting the understanding of Islam in the West and for his conciliatory stance during the recent cartoon controversy.
Before awarding the prince, Tantawi quoted Charles' views on Islam, which he described as the fruit of "serious study".
Charles had in the past urged the West to lay aside its "unthinkable prejudices" against Islam, pointing out that "extremism is no more the monopoly of Islam than it is the monopoly of other religions".
The decision to award the prince the degree had earlier prompted criticism from some of the institution's clerics, who argued that Charles had not earned the degree.
The prince and his wife arrived in Egypt on Monday afternoon for a visit intended to promote interfaith tolerance, sustainable employment and the prince's environmental initiatives.
Charles is expected to inaugurate the British University in Cairo, visit the western desert oasis of Siwa and lay a wreath at the Commonwealth cemetery at El Alamein, the site of a 1942 battle that was a turning point in World War II.
The royal couple leave on Friday for Saudi Arabia.