Gen Basbug is accused of leading a shadowy network of hard-line nationalists known as Ergenekon.
Prosecutors say they plotted to overthrow Prime Minister Recep Tayyip Erdogan's government in 2003.
Gen Basbug is on trial in Silivri prison, near Istanbul, where he and fellow alleged conspirators are being held.
On Tuesday he repeated his demand for the case to be held by the supreme court, a request rejected the previous day by the prison court.
'An injustice' Gen Basbug told the court he had no respect for the indictment, saying the allegations were against the Turkish armed forces and were a serious insult to the state.
"I regard it as an injustice to the Turkish armed forces and the rank which I held in it to make a defence in your presence," he said.
"Hence I will not defend myself and I will not answer any questions."
The general served as chief of staff from 2008 to 2010.
Around 40 spectators in the court reportedly applauded his words.
History of coups During the court's afternoon session, Gen Basbug rebuked the judges for allowing the prosecution to use tapes of phone conversations, Reuters news agency reports. He is then said to have left the court-room using a door reserved for defendants.
Turkish media report that the judges called a short recess and the trial continued shortly afterwards.
Turkey's military, the second largest in the Nato alliance after the US, has long seen itself as the guarantor of the country's secular constitution.
It staged three coups between 1960 and 1980 and has a history of tension with Mr Erdogan's governing Justice and Development (AKP) party.
The two sides have been locked engaged in a war of words for the past two and a half years over the plot allegations.
Critics complain that the Ergenekon investigation has focused on opponents of the AKP, which has Islamist roots. The government denies bias.
The AKP is considered a successor to the Welfare Party, an Islamist party which led a 1996-97 government forced to resign by an army-led campaign.