The audience at the pope's summer residence of Castel Gandolfo near Rome came two weeks after the pontiff stoked Muslim anger around the world after a speech he gave contained negative remarks about Islam.
It also came at the start of the monthlong celebration of Ramadan, a symbolic moment that the pontiff acknowledged as he expressed his "total and profound" respect for Islam.
The gathering was the Vatican's latest attempt to limit the damage following the pontiff's speech in his native Germany on September 12.
In that speech, the pontiff cited 14th-century Byzantine Emperor Manuel II Palaeologus as saying, "Show me just what Muhammad brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached."
Following the outcry from the Muslim world, the pope issued an expression of regret, saying his intention had been to provoke discussion, not offense.
"Unfortunately, this quote was capable of being misinterpreted," he said, "but to the careful reader of my text, it is clear that I in no way wanted to make mine the negative words pronounced by the medieval emperor in this dialogue, and their polemical content does not reflect my personal conviction."
But many Muslim leaders say that is not enough and they have expressed disappointment that the pope chose not to retract his speech unequivocally.
The meeting at Castel Gandolfo was billed by the media as a chance for dialogue between representatives of the two faiths.
In reality, though, the meeting was more like a papal audience, with the ambassadors seated around a small hall, listening to the pope's remarks -- before being thanked and ushered out.
The pope repeatedly emphasized his great respect for Islam and his desire to build bridges between the faiths.
He did, however, emphasize the need for reciprocity -- including religious freedom -- in relations between Muslims and Christians. This is a major issue for the Vatican. In some Muslim countries, such as Saudi Arabia, non-Muslims cannot worship openly.
In what appeared to be a reference to radical Muslim suicide bombers, the leader of the world's Catholics said all religious leaders had a duty to emphasize the sanctity of life to their followers.
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