Pope Benedict says the "the ideological manipulation of religion," sometimes for political ends, has led to tension, division and violence in society.
Speaking Saturday to Muslim leaders and other dignitaries at a mosque in Jordan's capital, Amman, the pontiff said religion should be a force for good, not division.
He urged Christians and Muslims to be "faithful worshippers of God."
The top religious advisor to Jordan's king, who is also his cousin, Prince Ghazi Bin Mohammed thanked the pope for expressing regret for remarks he made in 2006 about a centuries-old criticism of Islam.
But some Muslim clerics say they are disappointed the pontiff failed Saturday to make a new apology for the remarks.
Pope Benedict is on a Middle East tour in which he is trying to reach out to Muslims and Jews, both of whom have had strained relations with him since he became pontiff in 2005.
His trip to the region is being billed as a pilgrimage to the Holy Land.
Earlier Saturday in Jordan, the Roman Catholic Church leader called for mutual respect and cooperation between Christians and Jews. Earlier this year, the pontiff angered many Jews by reinstating an ultraconservative bishop who denies the Holocaust.
Members of Jordan's conservative Muslim Brotherhood are boycotting the pope's visit, still angry over his 2006 quotation of a criticism of Islam. The pontiff cited a 14th century Christian emperor who called some of the Prophet Muhammad's teachings "evil and inhuman." Later that year, he visited a mosque in Turkey, a gesture some say helped calm the outcry over his remarks.
The pope will celebrate Mass at a sports stadium in Amman Sunday. His Middle East tour also includes stops in Israel and the Palestinian territories.