Reports from the Anatolia news agency, which is run by the state, say the 968-page indictment accuses the suspects of taking part in an alleged conspiracy in 2003, codenamed "Operation Sledgehammer", with the aim of causing havoc in the country to pave the way for a military take over.
“Operation Sledgehammer” reportedly planned to bomb mosques and provoke tensions with Greece.
According to the news agency, the plan was drawn up at the base of the First Army in Istanbul, just after the Justice and Development Party (AKP) came to power in November 2002.
The Hurriyet newspaper says that those held on charges include 30 serving or retired military officers and that the First Army's former top general Cetin Dogan is the chief suspect. Former navy chief admiral Ozden Ornek, former air force commander general Halil Ibrahim Firtina, and the former number two of the general staff, retired general Ergin Saygun, have also been charged.
Although no date has been set for the trial, the indictment accuses all the defendants of "attempting to overthrow the government or prevent it from carrying out its duties through the use of force and violence", a crime which is punishable by 15 to 20 years in prison.
The government has denied accusations that it is looking to damage the secular order, describing the move as a step towards improving Turkish democracy.