All three could face up to ten years in prison should the judge at Tokyo District Court choose to punish them to the full extent of the law.
Kikukawa took responsibility for the scandal that rocked the camera hardware industry, stating in court that he regrets not revealing the cover-up earlier.
"There is no mistake. The entire responsibility lies with me," he said, going on to apologise to Olympus customers, investors, employees and the general public.
The scandal came to light last year when former Olympus chief executive Michael Woodford raised queries about accounting discrepancies, only to be dismissed by Kikukawa, who sought to keep the matter under wraps.
A subsequent investigation revealed that losses of up to $1.7bn (£1.1bn) had been covered up dating back to the 1990s.
Kikukawa was arrested in February this year, along with former executive vice president Hisashi Mori and former auditing officer Hideo Yamada. The three were indicted for the suspected violation of the Financial Instruments and Exchange Act.