Benedict used his weekly public audience to state his "deep respect" for Islam. This is the Vatican's fourth public expression of regret for the remarks.
However, Muslims around the world continue to urge the pope to make a clear apology for quoting 14th-century Byzantine Emperor Manuel II Palaeologus as saying that everything the Prophet Muhammad brought was evil, "such as his command to spread by the sword the faith he preached."
The pope, speaking in Italian to pilgrims at the Vatican, repeated his earlier remarks that the uproar was caused by a misunderstanding.
"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."
On the contrary, the 79-year-old leader of the world's 1 billion Catholics said the intention of his lecture at the University of Regensburg in Germany on September 12 had been to encourage religious dialogue.
"Beginning with what Manuel II subsequently says -- in a positive way, and with very beautiful words about how rationality must help guide the spread of faith -- I wanted to explain that religion and violence do not go together, but religion and reason do," he said.
The pope added that he hoped the uproar could serve to encourage "positive and even self-critical dialogue, both among religions as well as between modern reason and the faith of Christians."