By Christian Fraser
BBC News, Castel Gondolfo, Rome
Pope Benedict XVI has met Muslim ambassadors and representatives at his summer palace outside Rome, in an effort to mend diplomatic relations.
Muslim ambassadors from some 20 countries attended the meeting
It was the first time the Pope had been able to put in person an apology which he has now made in public on three occasions.
Amid tight security at Castel Gondolfo the ambassadors from some 20 countries attended.
They included the ambassador for Morocco, who has recently returned to Rome having being recalled by the King of Morocco in the wake of the controversy.
Others present were the ambassadors from Iraq, Lebanon, Jordan, and Turkey - the country the Pope will visit in November.
There were also representatives from the Islamic groups in Italy, that have advised the government on integration.
In his speech the pope did not specifically mention the quote that had angered Muslims worldwide, saying the circumstances that made the meeting necessary "are well known".
"Christians and Muslims must learn to work together," he said, "in order to guard against all forms of intolerance and to oppose all manifestations of violence".
That dialogue he said was not "an optional extra".
"I sincerely pray," he added, "that the relations of trust which have developed between Christians and Muslims over several years, will not only continue, but will develop further in a spirit of sincere and respectful dialogue".
The Pope had prepared his speech over the weekend with the help of the French cardinal Paul Poupard who is the Vatican's head of inter-faith dialogue.
Sometimes the Pope is criticised for not using the expertise around him.
Perhaps Cardinal Poupard's presence today signifies a change in thinking.
'Time and truth'
Several of the envoys who attended said they considered the meeting had gone a long way to help end the controversy.
The Iraqi ambassador to the Holy See, Albert Edward Ismail Yelda said he was satisfied with the speech. "I pray to almighty God the crisis will be behind us," he said.
"I was impressed by what the Pope had to say today.
"This is a pope for us all - I hope he is now a pope that works for the good of us all.
"Muslims were offended by his speech and they took to the streets to demonstrate that anger. That is called freedom of expression. Now Muslim leaders realise its time to put the past behind us and move forward.
"This was a day of reconciliation," he added. "It will not be healed in a day, but with time and truth on both sides, the bridges can be rebuilt."
Mario Scialoja, an adviser to the Italian section of the World Muslim League who also attended, endorsed those sentiments.
"It was a very good and warm speech," he said.
"He recalled the differences but expressed his willingness to continue cordial and fruitful dialogue," said Mr Scialoja.
Today's meeting shows the Pope is keen to foster closer ties with Islam. He has already stated that the two religions share one God.
But both sides have taken very clear positions on where this debate should start.
Pope Benedict wants to see reciprocal respect for those Christians worshipping in predominantly Muslim countries.
And Muslim representatives say discussions must be conducted on an equal footing. "We can't start from a position where Christianity is viewed as superior to Islam," said one.
The Pope's trip to Turkey still looks like it will go ahead and in light of the recent controversy it perhaps takes on added significance.
Today the Pope has received a sympathetic ear - but his first visit to a predominantly Muslim country may well be a much tougher proposition.