When he was first detained on November 19, Ghosn was charged with falsifying financial reports and under-reporting his income by about five billion yen (Â£34 million) over five years.
Greg Kelly, another Nissan executive, and Nissan as a legal entity were charged along with Ghosn with additional under-reporting of income, from 2015 to 2017.
Kelly and Nissan were not charged with breach of trust. Those allegations centre on Ghosn's handling of investment losses and payments made to a Saudi businessman.
Sixty-four-year-old Ghosn said he is innocent, and his lawyer has said he will seek the former chairman's release on bail.
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Suspects in Japan are routinely held for months until trials start.
Tokyo prosecutors say Ghosn, a Brazilian-born Frenchman of Lebanese ancestry, is a flight risk.
Earlier this week Ghosn told a Tokyo court he was innocent, in his first public appearance since his arrest, and appealed for his detention to end. But the court rejected the request.
"I have a genuine love and appreciation for Nissan," Ghosn told the court.
"In all of my efforts on behalf of the company, I have acted honourably, legally and with the knowledge and approval of the appropriate executives inside the company."
He said the compensation was never decided on, the investment deal did not result in any losses to Nissan, and the payments to the Saudi businessman was for legitimate services related to dealers and investments in the Gulf.
Ghosn, who appeared much thinner than before his arrest, came down with a fever the day after his court appearance, but has since recovered, his lawyer Motonari Ohtsuru said.
His wife Carole Ghosn has issued a statement expressing concern over his illness.
"I am pleading with the Japanese authorities to provide us with any information at all about my husband's health. We are fearful and very worried his recovery will be complicated while he continues to endure such harsh conditions and unfair treatment," she said.
Before his sudden downfall, Ghosn was a respected figure in the global car industry, having rescued the Japanese firm from near-bankruptcy, building its sales operations and profits and pioneering ecological vehicles.
Nissan said an internal investigation began in the middle of last year after whistleblowers came forward.
Chief executive Hiroto Saikawa has denounced Ghosn, accusing him of using company money and assets for personal gain.
Ethics officials at Nissan's alliance partner Renault SA of France concluded this week that financial compensation to members of the French carmaker's executive committee in 2017 and 2018 was fraud-free.
The review was initiated after Ghosn was arrested. Ghosn remains CEO of Renault.