The charges were the latest to emerge from an investigation into the so-called Ergenekon network, an alleged clandestine organisation set up by elements of the country's security services to defend Turkey's secularist foundations.
Details of the alleged plot to topple the government were first published by the Taraf newspaper in November 2009.
According to the plan, dated March 2009, the suspects would carry out bomb attacks in minority-populated neighbourhoods in Istanbul and the western city of Izmir.
They would also kidnap and assassinate prominent members of the communities.
The suspects planned to blame Islamist fighters for the attacks, thus increasing pressure on the Islamic-rooted government and paving the way for its overthrow, according to Taraf.
Media reports said that the case could be merged with two other cases in which 31 suspects, most of them navy officers, stand accused of an alleged plot to kill two admirals and blow up a submarine displayed in an Istanbul museum.
Scores of others defendants, including civilians and military figures, are already on trial as part of the investigation into the Ergenekon network.
Last month, prosecutors also charged 40 military figures in a separate investigation into an alleged 2003 army plot to topple the AKP.
The government says the investigations will help to improve democracy but secularists have accused the government of using the courts to intimidate them.