The organisers who had included a visit to the town of Regensburg on the banks of the River Danube thought that it would be a gentle diversion for Pope Benedict XVI, who agreed to address scholars at the local university before continuing on his tour of the German hinterland.

But the homily given by the former Cardinal Joseph Ratzinger on Tuesday has provoked a firestorm of Islamic rage and left in doubt his eagerly anticipated trip to Turkey later this year, which was intended to improve relations between Christians and Muslims.

Yesterday effigies of the Pope were set alight in Pakistan and hundreds joined protests in countries from Indonesia to Lebanon.

Presidents, prime ministers and religious leaders urged the Vatican to issue an apology.

At the Vatican the Pope’s senior advisers were mystified by the extraordinary scenes, which were eerily reminiscent of the protests over cartoons that appeared in Danish newspapers last year depicting the Prophet Muhammad. Then, as now, the reaction was slow to develop, and was stoked by an aggressive internet and e-mail campaign that urged Muslims to take to the streets over what was described as a most vile slur on Islam.

Attempting to dampen down the flames, the Vatican claimed that the Pope had been quoted out of context. In his Regensburg speech, he had referred to a dialogue on Christianity and Islam between Manuel Paleologus II, the 14th century Byzantine Christian emperor, and an educated Persian.

He said: “The emperor comes to speak about the issue of jihad, holy war. He said, and I quote, ‘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’.”

The phrases on Islam were “brusque”, he said, and he pointed out several times that he was quoting the emperor, not endorsing him. Yet insiders were left wondering whether he had deliberately raised the issue of Islamic extremism to provoke debate.

“Pope Benedict’s remarks about jihad may have been taken out of context but they were not an aberration,” said Father Federico Lombardi, the newly appointed Jesuit head of the Holy See press office. “On the contrary, they stem from his thinking about Islam and the West in the one and a half years since he became Pope.”

Father Lombardi added: “What emerges from an attentive reading of the text is a clear and radical rejection of the religious motivation for violence. It was certainly not the intention of the Holy Father to undertake a comprehensive study of the jihad and of Muslim ideas on the subject, still less to offend the sensibilities of Muslim faithful. Quite the contrary, what emerges clearly from the Holy Father’s discourses is a warning, addressed to Western culture, to avoid ‘the contempt for God and the cynicism that considers mockery of the sacred to be an exercise of freedom’.

“What is clear, then, is the Holy Father’s desire to cultivate an attitude of respect and dialogue towards other religions and cultures, including, of course, Islam.”

Although the desire for “respect and dialogue” is not in question, it has emerged that, six months after he succeeded John Paul II, Pope Benedict convened an unpublicised two-day conference on Islam, the West and Christianity at Castelgandolfo, his summer residence, attended by Western experts on the Muslim world.

At the end, according to Vatican insiders, the Pope concluded that it was time for a “more robust” approach to Islam, which in its “fanatical” or “violent” form posed a danger to the West. The problem with Islam, the Pope told delegates, was that unlike Christianity, which distinguished (in Christ’s words) between “that which is God’s and that which is Caesar’s”, Islam sought to “ integrate the laws of the Koran into all elements of social life”.

Whereas Jesus and the gospels offered a model to follow, the Koran was imposed rigidly with “no distinction between civil and religious law”. There was little spiritual or religious common ground, he is said to have told the conference. Therefore, Christianity could engage with Islam only as a “culture” and remind it to “respect human rights”, including the rights of Christian minorities in Muslim countries.

In May, the Pope told a Vatican conference on immigration that although he favoured “dialogue” with Islam it could only be conducted on the basis of “reciprocity”. Christians should “open their arms and hearts” to Muslim immigrants, but Muslims in turn had to overcome “the prejudices of a closed mentality”. As L’Espresso magazine observed yesterday: “This is not exactly a diplomatic pope.”

Since becoming Pope, the former Cardinal Ratzinger has been at pains to counteract the image he acquired as a ruthless enforcer of doctrinal orthodoxy when he was John Paul’s Prefect of the Congregation for the Doctrine of the Faith.

Once nickamed God’s Rottweiller, or the Panzer Kardinal, he has projected a gentler public face — making jokes, beaming from beneath his wavy white hair and even kissing babies as he meets crowds.

Many were pleasantly surprised when, in January, he chose the theme of love, sex and Christianity for his first papal encyclical. But he was elected in April last year over, say, a Latin American candidate because many cardinals were impressed by his insistence on the need to bolster Christian values not just in the Third World but also in Europe, which he believes is threatened by secularism, loss of faith — and Muslim immigration. As a cardinal, he was on record as opposing Turkish membership of the European Union. He has also, despite liberal Catholic hopes, so far shown no sign of relaxing doctrine to allow the use of condoms to prevent Aids in Africa.

In a little-noticed sign of his tougher line on Islam, in February he abolished the Council for Inter-Religious Dialogue, subsuming it into another council and dispatching its head, Archbishop Michael Fitzgerald, as his emissary to Egypt and the Arab League. The move was seen by many as a snub to Archbishop Fitzgerald, the most senior Briton in the Vatican, for his conciliatory approach to Muslims.

“It is difficult to imagine Benedict entering a mosque, as John Paul did in Damascus in 2001,” said Marco Politi, the Vatican correspondent of La Repubblica. Although he made overtures to Jews, Muslims and non-Catholic Christians after his election, and paid homage at Auschwitz in May, Pope Benedict lays less emphasis than his predecessor on dialogue with other faiths, let alone praying with or learning from them.

Vito Mancuse, lecturer in theology at the San Raffaele University of Milan, said: “The message of Regensburg is that logos — reason — is at the heart of Christianity, whereas the God of Islam is more arbitrary, and in the absence of reason lie the seeds of war. For Christians, God is love. Muslims don’t know what God is, only that he exists and dominates the world.”

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