Pakistan's parliament passed a resolution on Friday criticising the Pope for making "derogatory" comments.
The head of the Muslim Brotherhood said the Pope's remarks "aroused the anger of the whole Islamic world".
Pakistan's parliament passed a resolution demanding that the Pope retract his remarks "in the interest of harmony between religions".
"The derogatory remarks of the Pope about the philosophy of jihad and Prophet Mohammed have injured sentiments across the Muslim world and pose the danger of spreading acrimony among the religions," the AFP news agency quoted the resolution by the country's national assembly as saying.
The remarks prompted fears of unrest in Indian-administered Kashmir, as a result of which two separatist leaders were put under house arrest.
Meanwhile, the "hostile" remarks drew a demand for an apology from a top religious official in Turkey.
Ali Bardakoglu recalled atrocities committed by Roman Catholic Crusaders against Orthodox Christians and Jews, as well as Muslims, in the Middle Ages.
In Egypt, Muslim Brotherhood head Mohammed Mahdi Akef said the Pope's words "do not express correct understanding of Islam and are merely wrong and distorted beliefs being repeated in the West".
The 57-nation Organisation of the Islamic Conference also said it regretted the Pope's remarks.
Arab News has an in-depth article with various quotes from Muslim scholars. One Muslim professor's comments sum up the general argument:
Dr. Jameel H. Al-Lowahiq, professor of Shariah at the Taif University, said the remarks reveals “the enmity and grudge the new pope” harbors “toward Islam and our Prophet.”
“The lecture of the present pope, particularly at the time of deep international crisis, betrays the utter lack of prudence and propriety in sensing the consequences of making such a statement,” said Al-Lowahiq.
He added that that the pope was probably not aware of what the English philosopher Bernard Shaw said about the Prophet, in that the world badly needed a man like the Prophet Muhammad who placed his religion at an honorable position.
“I hope the pope will realize what Western and Christian historians wrote about Islam. The pope’s statement shows his and the entire Vatican’s weakness or rather nonexistent knowledge of Islam. It also reveals the psychological hatred the pope has of Islam and the Prophet,” added Al-Lowahiq.
“He should have more knowledge of Islam and the Prophet Muhammad, he is quoting a Byzantine ruler and ignoring the writings of honest Christian researchers who speak with credibility,” he said.
The Times of India has an article in which a valiant spokesman defends the Pope's comment. In the same article, a professor is not as kind in his assessment.
Fr Charanghat [the spokesman in Mumbai] pointed out that pulling a few lines from an eight-page speech meant for a specific audience of theology students had distorted its true meaning and intent, causing it to be labelled a "veiled attack on Islam".
He said the Pope was only trying to explain the reality of terrorism, more specifically jihad, as understood by extremists who are using it as a theological justification for violence.
"It was necessary to use the quote from a 1391 debate on Islam which would perhaps throw light on why a concept so rich as jihad as explained in the Koran was being misused by a minority of this great religion," he said.
Fr Julian Saldhana agreed the comments on Islam were part of the Pope's larger speech on faith and reason but felt that the quotation chosen was significant.
"The Pope has reproduced a quotation which is derogatory of the prophet Mohammed, without refuting it or showing that he disagrees with it," he said.
"I cannot agree with this comment, which is incorrect and lacking in sensitivity and respect. As for spreading Islam by the sword, we know that Muslim scholars, like Christian scholars, confronted with holy wars in the Old Testament in the Bible, know how to interpret the holy Koran in keeping with reason," he said.
And finally we have Pink News which started off with this:
The leader of the world’s largest Christian denomination has followed up his homophobic comments last week with alleged anti-Muslim remarks.
And that is a round-up of the thought processes that pervade modern intellectualism in the great universities and organizations of Islam (and the militant gay crowd in the UK).