The arrest and detention in the early hours of Friday morning of the former head of Turkey's military, General Ilker Basbug, signals an increase in tensions between the government and the military that looks certain to escalate further.
Basbug was arrested and interrogated for seven hours regarding allegations that he conspired as head of a secret organisation to overthrow by force the elected government of the Turkish Republic, before being imprisoned pending further questioning.
The arrest stems from a three-year investigation into the "Ergenekon" organisation. Prosecutors allege the group brought together serving and former senior military officers and civilian officials in a plot to overthrow the moderate Islamist government of Prime Minister Tayyip Erdogan.
The Ergenekon investigation has to date seen the arrest and charging of around 400 suspects, including 58 generals and admirals currently serving in the Turkish military, as well as dozens of intellectuals, academics, former and serving civil servants, and journalists.
It has been strongly supported by the government and by many secular Turks who share no ideological or religious platform with Erdogan's Justice and Development Party (AKP), and who believe the military and its associates have a case to answer.
But it has also been heavily criticised by Turkey's military and many secular Turks who regard it as a witch hunt against the military. The institution has traditionally guaranteed the secular nature of the Turkish republic in the face of what some Turks regard as the "creeping Islamization" of the country.
Many more though, fear that while the investigation may have begun in earnest, it has strayed beyond the limits of its scope and now threatens to undermine the very democratic process it was initiated to protect.
They criticise both the lack of clarity over what is being investigated and the length of time the cases are taking to resolve. In court for the first time last week after 11 months in jail, investigative journalist Ahmet Sik commented: "We don't even know what we are accused of; the indictment doesn't specify a crime."
With numerous trials related to the Ergenekon probe still ongoing, hundreds imprisoned and arrests still being made, tensions have been running high. Basbug's arrest comes little over a week after Turkish planes bombed a convoy of civilians smuggling cigarettes and diesel fuel into Turkey from Iraq, killing 35.
While Prime Minister Tayyip Erdogan expressed shock and grief at the killings and promised a full investigation, the military managed only a statement to the effect that it was acting on "intelligence" that the group were terrorists intent on attacking targets inside Turkey.
The Kurdistan Workers Party (PKK), which is recognised as a terrorist group by both the United States and the European Union, has for over two decades launched such attacks from bases in the autonomous Kurdish region of Northern Iraq.
However those killed were not terrorists but smugglers - many, of them also members of the "Village Guards," a state-run militia which guards against PKK activity in the region.
While neither the government nor the military has directly blamed the other side for the mistake which led to the killings, the respected Taraf newspaper has published unsourced claims that the intelligence supplied to the military came from Turkey's National Intelligence Organisation (MIT).
As a body which reports to the Prime Ministry, MIT has no direct connections with the military, and it has strenuously denied the allegations.
"MIT shared no intelligence on groups, locations, numbers, dates or routes that may have been related to the deaths of the 35 citizens," the organisation said in a written statement.
However the implications of the allegations appear clear: namely that a disagreement exists as to whether the faulty "intelligence" came from the military, or from sources controlled by the government.
Who exactly is responsible for the killings will hopefully emerge from the promised official investigation. But given the record to date of the Ergenekon investigation, few are betting that it can be completed either as swiftly or as openly as the tragic events would seem to require - or without further inflaming tensions between the government and the military.