Few people can have been more surprised – and alarmed – by the sudden influx of thousands of Syrian refugees across Turkey’s southern border than Recep Tayyip Erdogan, the Turkish prime minister.

Mr Erdogan, who was recently swept back into power in a third successive election victory, has spent most of the past decade establishing a cordial relationship with his Syrian counterpart, President Bashar al-Assad. The two countries have collaborated on military exercises, and even shared a joint cabinet meeting.

Until recently, the deepening alliance between the two had fuelled fears that a new, anti-Western axis was taking shape in the Middle East, in the form of Turkey, Syria and Iran. Damascus and Tehran have long been united in their opposition to Western interests in the region, and the suggestion that a key Nato ally such as Turkey might be lured into such an unholy alliance was greeted with deep concern by many in the West.

Turkey’s attempt to reposition itself as a regional power has been fuelled by thed economic development that has occurred since Mr Erdogan came to power in 2003.

With annual growth averaging 8 per cent, the boom times have given the Turks a new sense of confidence and pride. Mr Erdogan’s efforts to reassert his country’s historic influence in the region have certainly been popular with the public.

The sudden crisis in Syria, however, has brought this realignment to an abrupt halt. Mr Erdogan has been obliged to condemn the “brutality” of the Assad regime’s uncompromising response to the anti-government protests – which has not only dealt a mortal blow to their alliance, but created a humanitarian crisis on his own doorstep. Indeed, Turkey’s anger at the Syrian government has led to Ankara threatening to back Western calls for a UN Security Council Resolution condemning the crackdown – a move that would have been unthinkable just a few weeks ago.

Turkey’s denunciation of the Assad regime will also have repercussions for its new-found friendship with Iran, particularly since Tehran has been accused of sending detachments of its Revolutionary Guards to Damascus to ensure that its closest regional ally does not succumb to the protesters’ demands.

One of the reasons Turkey has embarked on this more assertive approach to its foreign policy, and wooed its less savoury neighbours, is Ankara’s frustration over the seemingly interminable obstacles placed in the way of its attempts to secure EU membership. Britain has consistently argued that the EU would be foolhardy to ignore Turkey’s pivotal position in the eastern Mediterranean. But Ankara’s attempt to join the European club has been bitterly opposed by Germany and France, which believe that the accession of a predominantly Muslim state would undermine the union’s cultural foundations.

As a result, rather than drawing closer to Europe, Turkey has launched a deliberate policy to strengthen its regional alliances at Europe’s expense. The rapprochement with Syria, for example, is a relatively recent development, in part motivated by Mr Erdogan’s desire to end Turkey’s strategic alliance with Israel.

Of course, as the head of Turkey’s Justice and Development Party (AKP), which has its roots in various Islamist movements, Mr Erdogan was never going to enjoy an easy relationship with Israel. After he became prime minister, relations between the two countries gradually deteriorated, with tensions boiling after following Israel’s military intervention in Gaza in early 2009. The Turks responded by organising the so-called “Gaza Freedom Flotilla”, which ended with nine activists being killed when they became involved in violent clashes with Israeli commandos trying to prevent them from reaching the Gazan coast.

Turkey’s deepening friendship with Iran is another example of the worrying international re-alignment that has taken place during Mr Erdogan’s eight years in power. Ankara’s attempt last year to derail the American-led effort to persuade Iran to freeze its nuclear enrichment programme caused deep irritation in Washington, and raised doubts about Turkey’s status as a key strategic partner in Nato.

That strained relationship was certainly in evidence at the start of the Libya crisis, when Ankara opposed Nato’s plans to launch a UN-backed military intervention to protect anti-Gaddafi rebels. Senior officers say the Turks have frequently intervened during the bombing offensive to prevent key Gaddafi targets from being attacked.

Many Western governments will now be hoping that the Syrian crisis prompts Ankara to reappraise its confrontational attitude, and work more closely with Europe and America on issues of mutual interest. The fact that the Turks last week hosted a conference of Syrian opposition figures certainly suggests the country is giving serious consideration to its regional alliances.

If that is indeed the case, then it would also be a good moment for EU leaders to reflect on where their own priorities lie. The political unrest throughout the Middle East that has been caused by the Arab Spring is likely to cause a great deal more instability in the months ahead. So it is very much in our interests that we ensure Turkey is allied to the EU, rather than falling into the orbit of rogue states such as Syria and Iran.