Pope Benedict XVI has said he is sorry that a speech in which he referred to Islam has offended Muslims.
The Vatican said the Pope's remarks had been misinterpreted
In a statement read out by a senior Vatican official, the Pope said he respected Islam and hoped Muslims would understand the true sense of his words.
In Tuesday's speech the Pope quoted a 14th Century Christian emperor who said the Prophet Muhammad had brought the world only "evil and inhuman" things.
The remarks prompted protests from Muslims around the world.
The BBC's Christian Fraser in Rome says the speed with which the Vatican has reacted shows just how seriously it views the situation.
Reading the statement, new Vatican Secretary of State Cardinal Tarcisio Bertone said the Pope's position on Islam was in line with Vatican teaching that the Church "esteems Muslims, who adore the only God".
"The Holy Father is very sorry that some passages of his speech may have sounded offensive to the sensibilities of Muslim believers," the statement said.
But Egypt's Muslim Brotherhood said the statement did not go far enough and called on the pontiff to apologise in person.
"The Vatican Secretary of State says that the Pope is sorry because his statements had been badly interpreted, but there is no bad interpretation," Abdel Moneim Abul Futuh, a senior official from the opposition party told AFP.
Our correspondent says the statement goes as far as it can towards an apology.
But the Pope is known to have strong feelings about the relationship between religion and violence and is thought unlikely to retract the sentiment of his speech.
There will still be concerns about whether to go ahead with the Pope's planned visit to Turkey in November, our correspondent says.
The BBC's David Willey in Rome says Pope Benedict, a theologian who has led a sheltered life in the Vatican for more than two decades, may not have understood the potential implications of his remarks.
He says the Cardinal Bertone, the newly-appointed top Vatican official, faces the task of serious damage control in the coming days.
Security at the Vatican is being stepped up, although the pontiff remains closeted with his closest advisers at his summer villa at Castelgandolfo near Rome.
In his speech at Regensburg University on Tuesday, the German-born Pope quoted Emperor Manuel II Paleologos of the Orthodox Christian Byzantine Empire.
Stressing that they were not his own words, he quoted the emperor saying: "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."
Street protests have been held in Pakistan, India, Turkey and Gaza
He also said that violence was "incompatible with the nature of God and the nature of the soul".
Reactions to the speech have come from such leaders as Pakistani President Pervez Musharraf, who said efforts to link Islam and terrorism should be clearly opposed.
Street protests have been held in Pakistan, India, Turkey and Gaza.
In the West Bank city of Nablus, two churches were firebombed on Saturday in attacks claimed by a group which said it was protesting against the Pope's remarks.
But German Chancellor Angela Merkel has come to the pontiff's defence, saying the aim of the speech had been misunderstood.