A dozen supporters of the military showed up later, expressing support for the defendants with placards saying "The heroes are inside [the court], where is justice?" and "Glory to the brave officers, the patriots."
Navy officers charged
The suspected plot, codenamed "Cage," allegedly involved plans to carry out bomb attacks in minority-populated neighbourhoods, notably Armenian, in the cities of Istanbul and Izmir, and to kidnap and assassinate prominent community members there.
The accused reportedly intended to blame the violence on Islamic fundamentalists and create the impression that the AKP encouraged religious extremism, hoping to pave the way for the party's overthrow.
A document alleged to detail the plans was published in December 2009 by Taraf, an independent Turkish newspaper.
The suspects, including 29 navy officers and a civilian, face up to 15 years in jail for "membership in a terrorist organisation".
The most senior defendants at Tuesday's trial included Kadir Sagdic, a three-star admiral and commander of the Turkish navy's Mediterranean flank, Mehmet Fatih Ilgar, a one-star admiral and Feyyaz Ogutcu, a retired three-star admiral.
The court will decide whether to merge the case with the trials of other navy officers, accused over an alleged plot to kill two admirals and blow up a submarine on display in an Istanbul museum.
Agos, a bilingual Turkish-Armenian weekly, will also argue that the murder of Hrant Dink, an ethnic Armenian journalist shot dead by a nationalist youth in 2007, was part of the "Cage" plan.
A total of 290 people have been charged so far in relation to the probe into Ergenekon, under way since June 2007.
The investigation was initially seen as a success in a country where the army has unseated four governments since 1960.
However, its credibility decreased as prosecutors began targeting academics, journalists and writers known as AKP critics, and defendants accused police of doctoring and fabricating evidence.
The probe has deepened the rift between Turkey's secularists and the AKP, with critics saying it has degenerated into a government-sponsored campaign to bully and silence opponents.