General Ilker Basbug, 68, is one the most senior officer to face trial in the anti-terror probes that began years ago.
The government has said the inquiry, which has seen hundreds arrested is a triumph for the rule of law and democracy, but some have accused it of score-settling, long imprisonments without verdicts and other lapses have tainted the legal process.
Basbug was arrested and placed in a prison near Istanbul overnight on Thursday after seven hours of questioning by prosecutors investigating allegations that the military funded dozens of websites aimed at discrediting Prime Minister Recep Tayyip Erdogan’s government in 2009. Basbug, who retired in August 2010, led the military at the time.
Basbug’s lawyer, Ilkay Sezer said his client has denied accusations during questioning.
The alleged conspiracy involving Basbug was first reported by a Turkish newspaper in 2009, which printed a photocopy of an alleged plan to damage the reputation of the government by portraying it as corrupt.
Investigations into the reported conspiracy were inconclusive because the original document, allegedly signed by a navy colonel, could not be found.
But the probe was revived last year after an unidentified military officer allegedly sent the original document to Istanbul’s chief prosecutor.
Some suspects already charged in the case, including senior generals and admirals, have proclaimed their innocence and said they acted in a chain of command.
“If I am being accused of bringing down the government with a couple of press statements and one or two internet stories, this is very bitter,” local media quoted Basbug as saying. “If I had such bad intentions, as the commander of a 700,000-strong force, there would have been other ways of doing it.”
Basbug told journalists before being taken to prison: “The 26th Chief of Military Staff of the Turkish Republic is being accused of forming and leading a terror organisation. I leave it up to the great Turkish people to decide.”
Hundreds of people are already on trial accused of terrorism charges for alleged involvement in separate plots that prosecutors say were aimed at destabilising Turkey amid suspicions by military-backed, secular elites that a government led by pious Muslims planned to impose religion on society.
Erdogan’s aides describe themselves as conservative democrats and have maintained close ties with the West while seeking to represent the views of the Muslim world.
President Abdullah Gul, who survived a military attempt to derail his presidential candidacy in 2007, said the “independent courts” would implement the law in Basbug’s case..
“No one can be pronounced guilty before a court decision. I would like everyone to know this,” he said. “Everyone is equal before the law. That’s why we must follow the process calmly.”
Gul has in the past expressed concern about reports of prisoners languishing without verdicts, a chronic problem for Turkey’s courts.
“It has always been the spokesperson of the powerholders of the time and it has always been under the tutelage of their ideology,” he said.
The military says 58 serving generals or admirals are in jail. Last year, the nation’s top four military commanders, including the chief of staff who succeeded Basbug, resigned in protest against the arrests and prosecutions of military officers.
Turkey’s military has long seen itself as a guardian of the country’s constitution and staged three coups between 1960 and 1980.