Pope Benedict told Muslim envoys on Monday that Christian and Muslim believers must reject violence.
The Pope expressed his "esteem and profound respect" for members of the Islamic faith in a meeting with diplomatic envoys from some 20 Muslim countries plus the leaders of Italy's own Muslim community at his summer residence Castelgandolfo.
"Christians and Muslims must learn to work together ... in order to guard against all forms of intolerance and to oppose all manifestations of violence," said the 79-year-old Pope.
It was the fourth time he had tried to make amends to Muslims, without actually apologising directly, for a speech at a university in his native Germany on September 12.
The leader of more than one billion Roman Catholics has expressed regret at the response to his quoting 14th-century Byzantine Emperor Manuel II Palaeologus, who said the Prophet Mohammad commanded his followers "to spread by the sword the faith he preached".
The Pope said that his intention was to explain that religion goes together with reason, not with violence.
His speech to Muslim envoys, delivered in French but also immediately made available by the Vatican in Arabic, made repeated references to the need for dialogue between faiths.
Mario Scialoja, an adviser to the Italian section of the World Muslim League who attended the audience, said afterwards that he thought it was a "very good and warm speech"
"He recalled the differences but expressed his willingness to continue in a cordial and fruitful dialogue, said Scialoja, who added that he "had not been expecting another apology".
The envoys invited included those from major Muslim countries such as Indonesia, Egypt, Pakistan, Turkey, Iran and Iraq, plus the Arab League.
Thousands of Muslims demonstrated against the Pope after last Friday's prayers at mosques around the world, but the anger and the size of the protests appears to be diminishing.
The Pope is facing the toughest international crisis since his election in April, 2005, and the vehemence of some reactions has raised doubts about a planned trip to Turkey in November.
Mehmet Ali Agca, the Turk who tried to kill Pope John Paul II in 1981, warned Benedict not to travel to Turkey, saying his life would be at risk.