Basbug spent two hours with reporters, telling them the military supports Turkish democracy, The New York Times reported.
More than 100 defendants, including retired generals, have been on trial for several months, charged with plotting to overthrow the government of Prime Minister Recep Tayyip Erdogan. The suspects, who also included journalists, professors and other intellectuals, are accused of belonging to an illegal ultranationalist group called Ergenekon.
"As the Turkish armed forces, we are loyal and respectful of democracy," Basbug said. "No one undergoing activities against the present democratic regime in Turkey can exist or find shelter within the Turkish armed forces."
The military has a history of carrying out coups, with four taking place between 1950 and 1997.
The investigation that led to the current trial allegedly turned up several underground weapons caches in several Turkish cities, including a military area. Basbug denied the weapons belonged to the military.
However, four military officers on active duty were arrested last week in connection with weapons discovered in Istanbul.