The Vatican has denied that Pope Benedict XVI intended any offence to the Muslim religion, after a speech touching on the concept of holy war.
Muslims in Pakistan staged an anti-Papal protest
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.
The remarks have angered clerics and commentators around the Muslim world.
However, the Vatican said the Pope had wanted to make clear that he rejected violence motivated by religion.
The pontiff had not intended to offend Muslims, the Vatican said.
"It certainly wasn't the intention of the Pope to carry out a deep examination of jihad (holy war) and of Muslim thought on it, much less to offend the sensibility of Muslim believers," said chief Vatican spokesman Federico Lombardi in a statement.
"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."
But the statement has failed to quell criticism. In developments around the world:
- Pakistan summoned the Vatican's ambassador to express regret over the remarks, as parliament passed a resolution condemning the comments
- The head of the Muslim Brotherhood said the remarks "aroused the anger of the whole Islamic world"
- Palestinian Prime Minister Ismail Haniya condemned the Pope's comments
- In Iraq, the comments were criticised at Friday prayers by followers of radical Shia cleric Moqtada al-Sadr
- Salih Kapusuz, deputy leader of Turkey's ruling AK party, likened the pontiff to Hitler and Mussolini
- The 57-nation Organisation of the Islamic Conference said it regretted the Pope's remarks
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.
Correspondents say 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.
The Vatican is seriously concerned that the protests might develop into violence directed at the tiny city state, says the BBC's David Willey in Rome.
But preparations for the Pope's forthcoming visit to Turkey, a predominantly Muslim secular nation, in 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."