Two other former executives, as well as the camera firm itself, filed a guilty plea in Tokyo District Court.
They face up to 10 years in prison.
The three admitted to hiding losses dating back to the 1990s, which were brought to light by a former chief executive, Michael Woodford.
'Entire responsibility'
Mr Kikukawa said he regretted not revealing the accounting irregularities earlier.
"There is no mistake. The entire responsibility lies with me," Mr Kikukawa said in court on Tuesday.
He also apologised for the trouble caused to investors, customers, employees and the general public.
The scandal was revealed when Mr Woodford, the British chief executive, was dismissed from his post after he challenged Mr Kikukawa and the board over suspiciously large payments related to acquisitions.
An investigation was launched that revealed a cover-up of losses.
Mr Kikukawa, former executive vice-president Hisashi Mori and former auditing officer Hideo Yamada were arrested in February and later indicted on suspected violation of the Financial Instruments and Exchange Act.
Former Olympus chairman Tsuyoshi Kikukawa has pleaded guilty to charges of falsifying accounts, covering up losses of $1.7bn (Â£1.1bn), at the opening of his trial.