Prime Minister Tayyip Erdogan's Justice and Development Party, AKP, which itself has Islamist roots, has made curbing the military's political influence one of its main missions, and state prosecutors have pursued officers suspected of conspiring against current and former governments.
The arrests of a top retired general and several other officers for questioning was the latest humiliation for generals who for decades had considered it their right to interfere in political affairs and had toppled four governments between 1960 and 1997.
Among those detained on Thursday was Major-General Erol Ozkasnak who, as Secretary General for the Chief of Staff, had been third in command at general staff headquarters when the military forced prime minister Necmettin Erbakan to quit.
Television footage showed police standing guard outside Ozkasnak's seaside mansion in Bodrum, one of Turkey's most desirable Mediterranean resorts, while more police searched inside.
A picture on the website of state-run Anatolian news agency showed a silver-haired Ozkasnak wearing sunglasses and being led from his home followed by a man in a suit, apparently a plain-clothes police officer.
Prior to his arrest, Ozkasnak emerged from his house to collect something from his car. "Please don't disturb me. I am going to be disturbed anyway in a little while," Anatolian reported him as telling reporters gathered outside his home.
Police swooped on the homes of the officers in several cities across the country, including the capital Ankara and Turkey's biggest city Istanbul, after a court issued the arrest warrants for four serving and eight retired officers.
Political reforms in 2010 to remove the immunity of old coup leaders gave prosecutors room to delve deeper into Turkey's history.
The sight of police seizing white-haired former generals and escorting them into detention, unthinkable a decade ago, has become a familiar one in Turkey over the last few years.
Hundreds of military officers, including top serving and retired commanders, are now facing trials accused of involvement in the alleged "Ergenekon" and "Sledgehammer" coup conspiracies against Erdogan and his ruling party.
An Ankara court ruled over the weekend that former deputy chief of staff Cevik Bir and other officers should be held under pre-trial detention relating to the 1997 "coup", to remove any risk of them fleeing.
Those arrested on Thursday will initially be brought in for questioning and a court will then have to rule whether they will remain formally detained. There is no provision for bail in Turkey and pre-trial detention can drag on for months.
The officers would face charges of plotting to remove an elected government and preventing it from fulfilling its duties.
Erbakan, who died of heart failure aged 85 in March last year, pioneered Islamist politics in Muslim but strictly secular Turkey and paved the way for the subsequent success of Erdogan's AKP.
The generals, known widely by their Ottoman title of "Pasha", traditionally saw themselves as the guardians of the secular republic set up by soldier-statesman Mustafa Kemal Ataturk from the ashes of the Ottoman Empire in 1923.
In the Sledgehammer case, where 365 serving and retired military officers are being tried over an alleged coup plot against Erdogan's government, defendants were expected to present their final defences on Thursday.
Instead, around 40 defendants launched a protest in court, wearing black t-shirts emblazoned with the slogan: "Justice against science, we want a fair trial" - apparently suggesting the judicial system had ignored scientific evidence presented by the defence.
Defendants say they have proved some of the evidence against them, such as computer files, was forged or fabricated. Another 70 defendants failed to appear in court and their lawyers were also absent on Thursday in protest against what they see as an unfair trial.
"We have been tolerant of you until now. You have crossed your legs, even turned your back before the court," Anatolian quoted one of the judges as saying, following a dispute with defendant Colonel Mustafa Onsel over the t-shirt protests.
"Sledgehammer" dates back to 2003, a year after the AKP came to power, stirring secularist fears of an Islamist takeover.
It allegedly included plans to bomb historic mosques in Istanbul and trigger conflict with Greece. Defendants say the prosecution documents were part of a war game scenario used in a military seminar and that other documents were faked.
Separately, this month the landmark trial began of former General Kenan Evren, now 94, who led a coup in 1980 that led to the execution of 50 people, the torture of thousands, and disappearance of hundreds more in three years of military rule.