The Vatican stepped in as anger built among Muslims over some of his remarks during his pilgrimage in Germany.
"It certainly wasn't the intention of the pope to carry out a deep examination of jihad (holy war) and on Muslim thought on it, much less to offend the sensibility of Muslim believers," said a Vatican spokesman.
The comments came from the Rev Federico Lombardi, who accompanied the pontiff on the trip, which outlined in a statement after Benedict returned to Rome.
A few hours earlier, Turkey's top Islamic cleric asked Benedict to apologise about the remarks and unleashed a string of accusations against Christianity.
The gaff has raised tensions before the Pontiff's planned visit to Turkey in November on what would be his first papal pilgrimage in a Muslim country.
Religious Affairs Directorate head Ali Bardakoglu, a cleric who sets the religious agenda for Turkey, said he was deeply offended by remarks about Islamic holy war and he called the remarks "extraordinarily worrying, saddening and unfortunate."
Bardakoglu said that "if the Pope was reflecting the spite, hatred and enmity" of others in the Christian world, then the situation was even worse.
International outrage at remarks
The Pope made his remarks on Islam in a speech in which he quoted from a book recounting a conversation between 14th century Byzantine Christian Emperor Manuel Paleologos II and an educated Persian on the truths of Christianity and Islam.
"The emperor comes to speak about the issue of jihad, holy war," the Pope said.
"He said, I quote, 'Show me just what Mohammed 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'," he quoted the emperor as saying.
Clearly aware of the delicacy of the issue, Benedict added, "I quote," twice before pronouncing the phrases on Islam and described them as "brusque," while neither explicitly agreeing with nor repudiating them.
In Egypt, Mohammed Mahdi Akef, the leader of Egypt's Muslim Brotherhood, also called for an apology.
Akef contended that the Pope's remarks "threaten world peace" and "pour oil on the fire and ignite the wrath of the whole Islamic world to prove the claims of enmity of politicians and religious men in the West to whatever is Islamic."
The 57-nation Organisation of the Islamic Conference, based in Jiddah, Saudi
Arabia said it regretted "the Pope's quote and for the other falsifications."
The OIC expressed hopes that "this sudden campaign does not reflect a new trend for the Vatican policy toward the Islamic religion."
Militant Islamic websites also unleashed a scathing campaign against the Pope.
The Pope's remarks have also sparked criticism from Pakistan where the country's parliament called on Pope Benedict to retract his controversial remarks linking Islam with violence.
In India the the head of the National Commission for Minorities said the Pope sounded like a medieval crusader.