Speaking last week at the University of Regensburg in his native Germany, Benedict cited a Medieval text that characterized some of the teachings of the Prophet Muhammad as "evil and inhuman," particularly "his command to spread by the sword the faith."
"This quote unfortunately lent itself to be misunderstood," the pontiff said in comments that he repeated in several languages.
"In no way did I wish to make my own the words of the Medieval emperor," he said. "I wished to explain that not religion and violence, but religion and reason go together," he added, drawing applause from the crowd.
On Sunday, Benedict said that he was "deeply sorry" over the reactions to his remarks and that they did not reflect his own opinions. But many in the Islamic world were not satisfied.
The pontiff's comments Wednesday during his weekly audience at the Vatican were part of a reflection over the Sept. 9-14 trip to his native Bavaria. Benedict said he wanted to share the "sentiments and feelings" he felt during his visit.
"I hope that in several occasions during the visit ... my deep respect for great religions, in particular for Muslims — who worship the one God and with whom we are engaged in defending and promoting together social justice, moral values, peace and freedom for all men — has emerged clearly," Benedict said.
Before the audience, the pontiff, riding in an open jeep, waved to the crowd in a tightly guarded St. Peter's Square. At the end, the pontiff remained in the piazza to be greeted by some of the faithful.
Security has been stepped up across Italy over the past days out of concern that Muslim anger following the pope's remarks could cause Roman Catholic sites to become terrorist targets.
Rome Prefect Achille Serra held a meeting with security forces Wednesday. However, he stressed that "there is no specific threat," according to the ANSA and Apcom news agencies.
Italian forces provide security to the Vatican, along with the Swiss Guard, which is responsible for the pope's personal safety.