The comment has called down the wrath of Muslim extremists and the shocked dismay of Islamic moderates. Threats have been issued not only to the papacy but the entire billion-strong community of Catholics. One popular jihadist website operated from Kuwait declared that Catholics “are doing everything in their power to extinguish the light of God” and called for violent retribution.

The Pope’s equivalent of a foreign minister, secretary of state Cardinal Tarcisio Bertone, read out an apology at a news conference in the Vatican yesterday, saying the Pope’s position on Islam was in line with Vatican teaching that the church “esteems Muslims, who adore the only God”. The Holy Father was very sorry that some passages of his speech may have sounded offensive to the sensibilities of Muslim believers, it said.

But the statement has sparked outrage throughout the Islamic world and called into doubt the likelihood, not to mention advisability, of his planned visit to Turkey in two months’ time.

There have already been violent protests in Turkey and the Middle East. Yesterday Palestinians wielding guns and firebombs attacked five churches in the West Bank and Gaza, including the Anglican church in Nablus, setting its front door ablaze. In Gaza City militants sprayed the facade of the Greek Orthodox church with bullets.

The Turkish prime minister, Recep Tayyip Erdogan, said yesterday: “The Pope spoke like a politician, not like a man of religion . . . In an era when a dialogue has been initiated between religions, values and civilisations, it is very unfortunate that these remarks have been made against Islam.” He added that he too was now uncertain whether Benedict should still visit Turkey.

Benedict has also, crucially, exacerbated deep divisions within his own church between traditionalist Catholics and moderate progressives. Those Catholics who had come to feel comfortable with the mild and elderly professorial Pope, relieved that “God’s rottweiler” was not about to declare jihad on the liberal wing of his own church, are utterly dismayed at this apparent show of Ratzinger’s ageing teeth.

In the lecture last Tuesday at the University of Regensburg, where he had once been a professor, the pontiff had been addressing the relationship between faith and reason, a favourite topic of Catholic theologians ever since the Middle Ages. In the intimate and academic confines of the lecture room, the Pope inserted that single incendiary sentence, quoting a medieval text referring to a debate between the Byzantine emperor Manuel II Palaeologus and a Persian Muslim.

“Show me just what Muhammad brought that was new,” he quotes the emperor as saying, “and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached.”

Defenders of the Pope’s quotation, starting with Father Federico Lombardi, the official Vatican spokesman, have tried to emphasise the context rather than the offending words. Lord Carey, the former Archbishop of Canterbury, argued that the Pope’s words had been misinterpreted. “Muslims must learn to accept criticism,” Carey said. “If the Pope quoted something from 600 years ago we should not assume this represents his view of Islam today.”

But the words will be remembered long after the context has been forgotten. The Pope had been pleading for all religionists to renounce violence, and arguing that there should be no gulf between religion and reason, suggesting that Islam was not a religion of reason — a theme he has emphasised in the past.

But his damaging words contain a startling lapse in historical accuracy, in the opinion of Muslim historians. It is commonly accepted that it was Islamic and Arabic culture that kept alive the philosophy of Aristotle through the Dark Ages and made the Catholic reconciliation of faith and reason possible in the work of Thomas Aquinas. One senior Anglican source said: “If anything, Islam was the religion of reason ahead of Christianity. Mathematics and medical science were developed in the Islamic world. The clash between reason and medievalism has Muslims on the side of reason.”

Moderate Muslim opinion is also baffled by the insensitivity of the Pope. Adnane Mokrani, a Rome-based Muslim theologian, said of the Pope’s quotation: “To use polemical texts from seven centuries back is not a suitable starting point, given that the current situation between Christianity and Islam is different.”

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