There are several plots being investigated, but General Ilker Basbug told Milliyet newspaper the investigation into the 2003 "Operation Sledgehammer" was the most serious.
Scores of officers were detained, including the former heads of the navy and air force, in the sweep launched by prosecutors in late February. While the two former service heads were released without charge, more than 30 others were charged.
Prosecutors have still to file the formal indictment.
The alleged actions included provoking a near-conflict with neighboring Greece and planting bombs in an Istanbul mosque.
"The incident is serious and up until now has perhaps had the most important effect on the Turkish Armed Forces," Basbug told the newspaper without elaborating.
Basbug in the past has spoken of the damaging effect on morale in the military that has resulted from the probes into anti-government plots. But he did not directly criticize the government or investigators in the interview.
Asked about Turkish media reports that commanders had threatened to step down following the arrests, Basbug said: "No, there was definitely nothing like this. It was not discussed, debated or expressed."
The officers under suspicion attended what the military has characterized as a war-games scenario, in which plans that could destabilize the government were mapped out.
In another alleged plot, a military prosecutor is carrying out a "comprehensive and multi-dimensional" probe of a colonel whose signature may have appeared on a document outlining a conspiracy to undermine the government, Basbug also said.
He declined to say whether any other serving officers are under investigation.
A military court last month rejected the prosecutor's request to arrest the colonel. He can only be dismissed from his post by the Defense Ministry if he is charged, Basbug said.
Turkey's generals have ousted four civilian governments in the last 50 years, but few observers believe they would take such action again, as Turks' confidence in democracy has grown and the government introduces European Union-inspired reforms.
But there are worrying signs of polarization.
Erdogan has threatened to call a referendum unless parliament approves planned constitutional changes to reform the judiciary, which along with the military is a stronghold of the conservative, secular forces who represent Turkey's old guard.
The row between the government and the secularist establishment has weighed on financial markets as investors fret about political stability in the $650 billion economy.
Source:reuters.com/
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