Fifty-one Turkish military officers, including two serving admirals, three retired admirals and three retired generals were last Monday arrested over an alleged 2003 plot - so-called 'sledgehammer' - to stir up chaos in Turkey and justify a military coup. A number of the officers have already been officially charged in court with the coup plan.

The arrests follow the publication last month of documents which allegedly showed that senior military officers had plotted a coup against the ruling AK Party, whose political roots lie in Islam. The latest alleged plot is similar to the reported 'Ergenekon' conspiracy a couple of years ago, in which military figures and secularists allegedly planned to create unrest, leading to a coup.

This latest action against the military, which has long been the guardian of the Turkish secular state - and the type of government established by modern Turkey's founder Kemal Ataturk - would have been impossible a few years ago. It shows that the government is now more confident of confronting the military head on, and that the army in Turkey is no longer untouchable.

The army has traditionally enjoyed a privileged place in Turkish society; it is generally well respected and is fiercely secularist. It has also overthrown or forced the resignation of four governments since 1960, the last time in 1997. The Turkish military has been looked upon not only as the protector of Turkish secularism but also as a bastion of stability and a counterbalance to political extremism in the country.

Military coups took place in 1960, 1971 and 1980, and in 1997 the army forced the then Islamist-led coalition government to resign because it feared it was trying to change the secular nature of Turkish politics and government. In the 1980 coup, the military took power after months of violence between left-wing and right-wing extremists nearly brought Turkey to the brink of civil war.

This particular coup stabilised the country and led it back along the path to a functioning democracy, but as is nearly always the case with military rule, human rights abuses certainly took place during this period.

Today the army leadership insists such coups are things of the past and that the latest alleged coup plot was nothing more than a planning exercise at a military seminar. Furthermore, there is no doubt that the army's power has been eroded over the years, not least because of Turkey's reforms carried out in connection with its EU membership bid.

However, the charges against so many senior military officers is certainly a huge test of the government's authority over the army. It represents another twist in the ongoing power struggle between the secular establishment, which includes the judiciary, and the governing AK Party, whose critics accuse of turning its back on Turkey's traditional secular system of government and wanting to turn the country into an Islamic state.

The Turkish government, led by Prime Minister Recep Tayyip Erdogan rejects such accusations, saying it simply wants to modernise Turkey and take the country into the EU. Ever since the AK Party was elected in 2002 and again in 2007, the military was faced with a new challenge, namely how to deal with a party which it suspects of turning its back on secularism but which remains popular throughout Turkey, and which has been praised at home and abroad for carrying out a series of political and economic reforms.

The army is indeed in a difficult position. It knows that both domestic and international public opinion will not accept a coup and that further confrontation with the government will probably only strengthen the ruling AK Party's popularity. It also has to face the fact that the recent arrests of so many of its senior officers represent a new level of boldness by the government in its attitude towards the military. So while the army still clings on to its traditional role as the guardian of the nation, it has to come to terms with the fact that its power is being gradually eroded.

The Turkish government's critics argue that this latest assault on the military is simply the AK Party's way of settling old scores with its rivals. It also raises questions about whether the staunchly secular military can peacefully co-exist with a ruling party that has Islamist roots.

There will always be an endless debate about whether the ruling AK Party is nothing more than a Muslim version of a modern Christian Democratic Party or whether it is presiding over a system of creeping Islamisation, evidenced, for example, by its attempt to overturn the headscarf ban in public buildings and the fact that in certain parts of Turkey one cannot buy alcohol any more.

If Turkey is to join the EU, it is quite clear that the army has to remain in its barracks and keep out of politics. There can be no compromise about that. However, any moves away from secularism in Turkey also raise eyebrows in Brussels.

How ironic, therefore, that until recently, Turkey's secular system was guaranteed by the country's military, which is being pushed back into its barracks by the EU.