Pope Benedict's remarks about Islam during a speech he delivered at his old university at Regensburg in Germany caused anger among some Muslims around the world, who considered them to be derogatory. A number of Muslim clerics and politicians even demanded a formal apology from the Pope.

The Pope quoted a 14th century Byzantine emperor - making clear that these were not his words - who had remarked: "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."

At face value these words sound insensitive at best and explosive at worst. However the Pope's point was to show the contradiction between religion and holy war. He has since explained that his words were taken out of context and misunderstood and that he was profoundly sorry for the reaction of some Muslims to his speech. The Pope also emphasised that he was simply quoting somebody, which did not imply that he agreed with the words in question.

I do not believe the Pope wanted to offend Islam nor do I believe that he should withdraw his remarks or apologise for them. A clarification was in order and that where it should have stopped, which in fact it did. What I do question, however - given the nature of relations between Islam and the West today - is the appropriateness of quoting something that was said seven centuries ago about Islam and which taken out of context has the potential to strain an already damaged relationship.

One is surely entitled to ask whether anybody at the Vatican anticipated the way the Pope's words might be taken out of context as well as the likely reaction. Was the Pope properly advised before he gave his speech? And what exactly did the Pope hope to achieve by quoting these words?

While it is true that most of the reactions to the quotation used to illustrate a philosophical argument were exaggerated - once again it looks as if extremists in the Muslim world hijacked this debate - some observers now suspect that the Vatican's policy on the Church's relations with Islam has changed.

Although Benedict XVI seems to be following in the footsteps of Pope John Paul II as regards the traditional teachings of the Church, there would appear to be a divergence in the Vatican's attitude towards Islam. This is not to say that this Pope is not in favour of a dialogue with other religions, such as Islam - he certainly is, and he has made this clear on a number of occasions. However, I think I am correct in believing that John Paul II - who became the first Pope to set foot in a mosque during a visit to Syria in 2001 - would not have thought it appropriate to use that quote.

Some Vatican watchers believe Pope Benedict wants to achieve better relations with Islam but this should consist of a frank and open debate. This debate, they say, should also include an emphasis on the rights of Christians in Muslim countries. Just as Muslims in the West enjoy complete freedom, so too should Christians enjoy the same freedom in the Muslim world.

This is certainly a reasonable attitude to adopt. Of course the Church should push for complete freedom for all Christians to practise their faith, including in Muslim countries. If this was not emphasised enough before, then Pope Benedict is correct to insist on this now. However, this freedom has to be achieved by careful diplomacy and genuine dialogue. Somehow I don't think the Pope's choice of a quote during his speech in Germany would have helped the plight of Christians in Muslim countries.

Pope Benedict needs to have advisers close to him who are knowledgeable on Islam. This is why some eyebrows were raised recently when the Pontiff decided to remove Archbishop Michael Fitzgerald, who ran a Vatican department that promoted dialogue with other religions and who was a distinguished scholar of Arab affairs and an expert on the Islamic world, and send him to Egypt as papal nuncio.

Fr Thomas Reese, a Jesuit scholar, told the BBC recently: "The Pope's worst decision so far has been the exiling of Archbishop Fitzgerald. He was the smartest guy in the Vatican on relations with Muslims. You don't exile someone like that, you listen to them.

"If the Vatican says something dumb about Muslims, people will die in parts of Africa and churches will be burned in Indonesia, let alone what happens in the Middle East. It would be better for Pope Benedict to have Mgr Fitzgerald close to him," he said.

Of course, the Muslim world, especially politicians and moderate clerics, have a duty to speak up in favour of dialogue and against extremism and violence. After the Pope's speech, churches were firebombed in the Palestinian territories, Indian and Pakistani Muslims burnt effigies of the Pope, an Italian nun was shot dead in Somalia and other violent protests took place in various Muslim countries.

Salih Kapusaz, the deputy leader of Turkey's ruling Justice and Development Party, accused the Pope of pitiful ignorance or a deliberate distortion of the truth and of trying to revive the mentality of the Crusades. This is all clearly unacceptable and one expects the voices of moderate Islam to be vociferous in its condemnation of such behaviour.

The Pope now has a very important chance to show his belief in a dialogue with Islam when he visits Turkey in November. This will not be an easy visit - as Cardinal Ratzinger he had spoken out against Turkey's membership of the European Union saying the country's culture was not compatible with Europe. This should be a very interesting visit indeed.