Absent from the first hearing were records of a National Security Council meeting from the day the coup began, Today's Zaman reported Tuesday.
The records of the Feb. 28, 1997, meeting had been requested by the court, but had not been sent by the council's legal department.
A 1,300-page indictment detailing charges against 103 current and former officers and a civilian was filed by June by the Ankara Public Prosecutor's Office following an investigation launched in 2012 into the coup.
The indictment seeks life prison terms for all of the suspects.
Some 38 suspects in the coup remain in jail pending trial.
Gen. Ismail Hakki Karadayi, former chief of the general staff, is charged with leading the coup.
Others charged include retired Gen. Cevik Bir, the former deputy chief of the general staff; retired Gen. Yalcin Ataman, the former commander of the 1st Army; and retired Maj. Gen. Erol Ozkasnak, former secretary-general of the general staff.