The trial of alleged plotters of "Sledgehammer" reflects a lingering mistrust between the traditionally secular military and a ruling party that critics say retains Islamist leanings.
Erdogan denies planning to roll back the secular constitution, and his AK Party goes into an election in June as firm favourite to win a third consecutive term, but the case is among a series of domestic and foreign policy challenges.
A court in Silivri, west of Istanbul, issued the arrest warrants for the defendants on Friday.
In total 196 officers are on trial, around three-quarters of them still serving, and most have been in and out of detention in the past year. Not all of them attended Friday's hearing. After the court served arrest warrants, 133 were taken for health checks before being escorted on Saturday either to the town's prison or, for those on active duty, a military prison in Istanbul. The remaining 29 were expected to surrender themselves at a courthouse in Istanbul on Saturday.
Television images showed a coach and two mini-buses taking the defendants to prison.
Concerns about political tensions are for now unlikely to unsettle investors, well-used to Turkey's turbulent political scene, so financial markets are not expected to move for now.
General Cetin Dogan, former commander of the prestigious First Army, and retired commanders of the navy and air force, Admiral Ozden Ornek and General Halil Ibrahim Firtina, were among the defendants that the court ordered to be arrested.
The trial, which began in December, was adjourned to March 14, and the chief judge pressed for an interim verdict to be read. Defence lawyers said their arguments were being overlooked and the arrests were unjustified. They objected to a change in judges during an earlier hearing.
"There is absolutely no risk they will escape. I have been an attorney for 33 years and I can't believe what's happening on this case, this is a travesty of justice," defence lawyer Sule Nazli Erol told CNN Turk.
The "Sledgehammer" plot allegedly involved plans to bomb historic mosques and provoke conflict with Greece, as part of a plan to undermine the government and enable a military takeover.
The defendants, important figures in NATO's second biggest army, deny any conspiracy and say the 'plot' was a war game exercise at a military seminar seven years ago. If found guilty, they could face 15 to 20 years in prison.
Since coming to power, the AK Party government has used reforms designed to boost Turkey's European Union membership bid to rein in the authority of an army that has toppled four civilian governments since 1960.
Erdogan has also driven an economic transformation which has shifted power to a new emerging business class and away from old elites made up of generals, judges and educators devoted to the secular vision of the republic's founder, Mustafa Kemal Ataturk.
Hundreds of defendants are already on trial at the same court in connection with a series of alleged coup plots allegedly orchestrated by the shadowy Ergenekon network.