Lawyers for the former jet-setting executive filed bail application hours later, but have acknowledged that he will probably be detained until a trial.
Ghosn denies any wrongdoing and argued in a dramatic first court appearance on Tuesday that he has been "wrongly accused and unfairly detained."
He was already facing a first charge for allegedly under-reporting his compensation over five years to the tune of five billion yen ($46 million) in official documents to shareholders.
Court grants bail to Nissan executive linked to financial misconduct
The charges filed today allege that the under-reporting continued for another three years.
And they include a charge of "aggravated breach of trust" over a complex alleged scheme in which Ghosn is said to have tried to transfer losses on foreign exchange contracts to Nissan's books.
As part of the scheme, he is accused of also using company funds to repay a Saudi acquaintance, who put up collateral for the contracts.
Prosecutors also filed charges Friday against Nissan and Ghosn aide Greg Kelly over the additional three years of under-reporting pay.
Nissan chairman arrested over financial misconduct
Ghosn has appeared in public just once since his shocking November 19 arrest, during the Tuesday court hearing called after his lawyers requested judges explain the tycoon's ongoing detention.
One of the most recognisable foreign executives in Japan, Ghosn was led into Tokyo District Court in handcuffs and with a rope around his waist and was noticeably thinner.
He spoke in a strong voice and said he had acted "honourably, legally and with the knowledge and approval of the appropriate executives inside the company".
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