A statement from the Vatican has failed to quell criticism of Pope Benedict XVI from Muslim leaders, after a speech touching on the concept of holy war.
The Pope's comments came on a visit to Germany
Speaking in Germany, the Pope quoted a 14th Century Christian emperor who said the Prophet Muhammad had brought the world only "evil and inhuman" things.
Pakistan's parliament passed a resolution on Friday criticising the Pope for making "derogatory" comments.
The Vatican said the Pope had not intended to offend Muslims.
"It is clear that the Holy Father's intention is to cultivate a position of respect and dialogue towards other religions and cultures, and that clearly includes Islam," said chief Vatican spokesman Federico Lombardi in a statement.
But in spite of the statement, the pontiff returned to Rome to face a barrage of criticism, reports the BBC's David Willey in Rome.
The head of the Muslim Brotherhood said the Pope's remarks "aroused the anger of the whole Islamic world".
Violence and faith
The controversy comes on an important day for the Vatican, with Cardinal Tarcisio Bertone, former Archbishop of Genoa, taking over as secretary of state.
Our correspondent says Pope Benedict, who has been closeted with his chief advisers at his summer residence near Rome, is upset at the way in which his remarks have been interpreted.
But there is no sense of panic at the Vatican, he says, and preparation for the Pope's forthcoming visit to Turkey, a predominantly Muslim secular nation, next November, are going ahead as planned.
In his speech at Regensburg University, the German-born Pope explored the historical and philosophical differences between Islam and Christianity, and the relationship between violence and faith.
Stressing that they were not his own words, he quoted Emperor Manuel II Paleologos of the Byzantine Empire, the Orthodox Christian empire which had its capital in what is now the Turkish city of Istanbul.
The emperor's words were, he said: "Show me just what Muhammad 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."
Benedict said "I quote" twice to stress the words were not his and added that violence was "incompatible with the nature of God and the nature of the soul".
"The intention here is not one of retrenchment or negative criticism, but of broadening our concept of reason and its application," he added in the concluding part of his speech.
"Only thus do we become capable of that genuine dialogue of cultures and religions so urgently needed today."
'Angry and hurt'
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.