Iranian President Mahmoud Ahmadinejad said: "We respect the Pope and all those interested in peace and justice," and said he accepted the Vatican view that the pontiff’s words had been "misinterpreted" and "taken out of context".

Malaysia’s Prime Minister Abdullah Ahmad Badawi said: "I suppose we could accept this. We hope that there would be no other statements that would anger Muslims."

Ali Bardakoğlu, the head of Turkey’s Religious Affairs Directorate said that Benedict’s "expression of sadness is a sign that he would work for world peace."

Australian Muslim leader Ameer Ali said Australian Muslims must "accept the Pope's apology" over remarks that offended Islam and "move on". Filipino Muslims expressed support for Pope Benedict's apology and blamed certain media outlets for increasing the tensions between Muslims and Catholics.

On 25 September 2006, Pope Benedict XVI held an audience with Muslim diplomats, ambassadors of Muslim countries and members of the Consulta Islamica, the Italian government appointed consultative body on Islamic affairs. The meeting was an effort to mend relations with the Muslim community. Pope Benedict's spokesman, the Rev. Federico Lombardi, said the meeting at Castel Gandolfo, the Pope's summer residence, was "certainly a sign that dialogue is returning to normal after moments of … misunderstanding."

During the session, Pope Benedict XVI reiterated his conviction that the dialogue between Muslims and Christians is "a vital necessity" for the good of a world marked by relativism, one that "excludes the transcendence and universality of reason." At this meeting, Pope Benedict expressed "all the esteem and the profound respect that (he has) for Muslim believers." Among the ambassadors invited were those from Iraq, Iran, Turkey, Morocco, as well as many other nations and Islamic groups.

Pope Benedict has taken another step to placate anger in the Islamic world over his remarks on holy war, making additions to his original text by re-affirming that a quotation from a 14th century Byzantine emperor was not his personal opinion. The original text said the emperor's remark was made "somewhat brusquely." The new version says that it was made with "a brusqueness that we find unacceptable." Pope Benedict added in a footnote:

In the Muslim world, this quotation has unfortunately been taken as an expression of my personal position, thus arousing understandable indignation. I hope that the reader of my text can see immediately that this sentence does not express my personal view of the Quran, for which I have the respect due to the holy book of a great religion.

He said he cited the text as part of an examination of the "relationship between faith and reason."