Two dozen people have been named as possible defendants, but several key figures, including the former armed forces chief, General Wiranto, are not among them.
He refused to leave his post, however, saying that only the armed forces chief of staff could dismiss him.
It had been widely thought that he would be named armed forces chief, a move that the United States opposed.
The fighting began a week ago when troops led by a former armed forces chief of staff tried to topple the Government.
General Sunthorn, who has been armed forces chief for nearly a year, had been due to retire in 1991.
His decision on the bases led to an angry walkout by his armed forces chief.
The armed forces chief of staff took the cue and ushered him from the palace.
He was promoted to armed forces chief of staff in 1973.
Of the 39 countries at the French-African meeting, 22 were represented by their armed forces chiefs of staff.
General Zia wants his constitution to be seen as more than a cloak for his personal rule as armed forces chief.