The Caliphate, the body that had governed the Muslim world for four centuries under the Ottomans, was unceremoniously abolished within months of the creation of the modern Turkish state.

The minarets of the country's mosques were silenced by a ban on the muezzin broadcasting their daily prayers, and the more radical madrassas were closed.

Anyone who turned up at Ankara's city walls in dress deemed to be too Islamic in nature was unceremoniously sent back to the provinces. Sharia law was replaced by a penal code modelled on that of Switzerland and the emancipation of women was encouraged by laws that banned the wearing of veils. Arabic script was replaced by the Latin alphabet, and the centuries-old ban on alcohol was lifted.

It is hardly surprising, then, that the crowds of demonstrators who have been protesting at the country's creeping Islamisation should carry banners bearing Ataturk's intimidating features.

The crude attempt by Recep Tayyip Erdogan, the country's crypto-Islamic prime minister, to secure the presidency for a practising Muslim, Abdullah Gul, the current foreign minister, has provoked such outrage that the nation's military elite, who regard themselves as standard-bearers of Ataturk's legacy, threatened to stage yet another military coup.

That deeply disturbing prospect has - for the moment, at least - been averted by Erdogan's decision to call an early election this summer to decide the issue by democratic means. But with Erdogan's Justice and Development party, which is deeply rooted in the country's burgeoning Islamic constituency, riding high in the polls, a return to the kind of military dictatorship that plagued Turkey's political development throughout the 20th century cannot be ruled out.

Turkey's military establishment is Kemalist to the core, and the mere suggestion that the country might appoint a president whose wife insists on covering herself with a veil for public functions would be enough to have them taking to their tanks.

Despite Erdogan's insistence that he has no desire to dilute the country's distinctive secular character, the hawkish generals have viewed him as an Islamist in disguise in the three years since he came to power. They, together with the millions of Turks who are at ease with the country's secular outlook, are concerned at the growing influence Islam is having on Turkish society.

Ten years ago it was normal to see groups of young girls in school uniforms on the streets of Istanbul. Today they have virtually disappeared, to be replaced by women wearing headscarves. During the holy Islamic month of Ramadan it is not uncommon for street fights to break out between religious Muslims objecting to their secular compatriots lighting a cigarette during the daytime fast.

Turn on any television or radio debate in Turkey these days and the main subject of discussion most likely concerns the threat Islam poses to the country's future. "Do you want us to become another Iran or another Afghanistan?" one frustrated secularist demanded of an Islamic supporter during a Turkish radio station phone-in earlier this week.

Given Turkey's geographical location, it is hardly surprising that it is susceptible to the threat of radical Islam being imported across its south-eastern borders. And even though Justice and Development's Islamic agenda is mild compared with that on offer in neighbouring Iran, Erdogan's failed attempt to criminalise adultery - it was vetoed by the current president, Ahmet Necdet Sezer - has done nothing to allay the suspicions of those determined to maintain the Kemalist settlement.

The mounting polarisation between Turkey's devout Muslims and its secular, mainly urban, elite should be a matter of grave concern for the West, which has often sent Ankara conflicting signals about its value as an ally.

In military and strategic terms, Turkey has long been regarded as a key asset, particularly after the September 11 attacks put it on the front line of Washington's various campaigns to root out Islamic terrorists and confront rogue states.

Yet Turkey's enthusiastic attempt to join the European Union has received a decidedly lukewarm response, with many member states expressing strong reservations about welcoming 70 million Muslims into an alliance whose population is more familiar with the tenets and traditions of Christianity.

The various delaying tactics Brussels has employed to postpone Turkey's entry, from doubts over its economic viability to Ankara's obstinacy about opening its ports to Greek Cypriot vessels, has not only succeeded in dampening the Turks' excitement about the whole venture, but has encouraged an upsurge in nationalistic fervour that underlies the country's current travails.

Accusations that the West's Islamophobia is responsible for blocking Turkey's entry to the EU have, perversely, increased support for Islamic groups that seek to accentuate the country's historic Muslim character.

Brussels' procrastination has also seen a revival of the ultra-nationalist groups that regard Cyprus as their cause célèbre, and are not afraid to use violence against anyone accused of "insulting Turkishness".

January's murder of Hrant Dink, the Turkish-Armenian journalist who accused the Turks of committing genocide against the Armenians during the First World War, is symptomatic of the paranoia and isolationism that is sweeping the country, and now threatens the long-term stability of a key Nato ally.

The EU's patronising treatment of Turkey's membership application has certainly not helped to placate this siege mentality, and explains why so many Turks now seek to invoke the spirit of Turkish nationalism espoused by Ataturk. But these are dangerous currents.

The generals, not the politicians, are the true keepers of the Ataturk flame and, like the country's founding father, they will not stand idly by if the Turks attempt a return to their old Islamic ways.