However, the pontiff did not apologize for the speech, as many Muslims around the world have demanded.
The pope said that the passages about holy wars that have caused offence were a quotation from a medieval text and do not "in any way" express his personal thoughts.
He also said the true meaning of his address was an invitation to "frank and sincere dialogue, with mutual respect."
Speaking at a German university on September 12, the Bavarian-born pope quoted a written criticism of Islam by Emperor Manuel II Palaeologus, who ruled the Orthodox Christian Empire from what is now Istanbul in the 1300s, in which he asks: "Show me just what Mohammad 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."
The Continuing Reverberations
The pope's speech has brought Muslims around the world out onto the streets in protest.
Morocco withdrew its ambassador to the Vatican on September 16, calling the Pope's remarks "offensive."
Speaking during an election rally in Sanaa on September 16, Yemen's President Ali Abdullah Saleh threatened to review ties with the Vatican unless the pope apologizes.
The Supreme Council for the Islamic Revolution in Iraq, one of the country's main Shi'ite political parties, has also called for the Pope to apologize "clearly and honestly."
The governments of Iran, Iraq, Egypt, and Kuwait summoned the Vatican's envoys to convey their protests.
The backlash over the Pope's comments had cast doubt on his planned visit to Turkey in November, with Turkish Prime Minister Tayyip Erdogan on September 16 calling the Pope's comments " unacceptable":
"I think it is unfortunate to talk about a religion and its prophet," Erdogan said. "It is unacceptable for the entire Islamic world. It should not be accepted in the Christian world as well."
In Russia, President Vladimir Putin on September 17 urged world religious leaders to show "responsibility and restraint." in televised comments, Putin said he hopes that "the leaders of the main world faiths will have sufficient strength and wisdom to avoid any extremes in relations between faiths."
Meanwhile Italy's news agency ANSA says the Italian interior ministry told police chiefs to raise the level of national security after receiving threats from Islamic groups over the pope's comments.
Security was also tightened at the Vatican ahead of Pope Benedict's regular Sunday blessing.