Prosecutors also filed charges Friday against Nissan and Ghosn aide Greg Kelly over the additional three years of under-reporting pay.
With each allegation against Ghosn, prosecutors can seek up to 22 days of detention to investigate the claims - the period for the aggravated breach of trust allegation expired Friday.
One of his lawyers later conceded that Ghosn could spend a further six months behind bars before his case comes to trial.
The court rejected an appeal by Ghosn's lawyers for his release from detention, and on Thursday turned down another appeal.
"I have a genuine love and appreciation for Nissan", Ghosn told the court. Nissan has dismissed Kelly from his role as a representative director.
The twists and turns since Ghosn's arrest have riveted Japan and the business world and the case is also being played out in local media, with another string of allegations leaking in the Japanese press Friday.
"I believe strongly that in all of my efforts on behalf of the company, I have acted honorably, legally and with the knowledge and approval of the appropriate executives inside the company - with the sole goal of supporting and strengthening Nissan, and helping to restore its place as one of Japan's finest and most respected companies". He also said the payments to the businessman, Khaled Al-Juffali, via a Nissan subsidiary, were compensation for taking care of hard business problems in the Middle East.
Nissan as well as Mitsubishi, the third alliance partner, have removed Ghosn as chairman, but Renault has kept him on while appointing a deputy CEO to ensure day-to-day management.
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At its own informal meeting, Renault said its directors were updated on the company's compliance investigation into payments to top executives.
"I am pleading with the Japanese authorities to provide us with any information at all about my husband's health".
This week he suffered a fever that prompted prosecutors to suspend their interrogations, though his lawyer said Friday that Ghosn's temperature had gone back down.
Ghosn holds French, Lebanese and Brazilian passports and his children live in the USA, his wife said that her husband is living in "harsh conditions" and enduring "unfair treatment", and that authorities have not let the family speak with medical personnel at the detention center.
The other new charge says Ghosn reported 2.9 billion yen ($26.9 million) in compensation, when he earned more than 7.1 billion yen ($65.7 million) in the three years ending in June 2018.
It said it took the charges filed against the firm "extremely seriously" and was continuing its investigation into the case.
That lack of transparency and concern that Nissan will use Ghosn's absence to push for more power within the alliance has heightened tensions between the two automakers.
The breach of trust charge alleges that 1.8 billion yen ($16.7 million) in damage was caused to Nissan through transactions made by Ghosn, and that $14.7 million was paid to the Saudi businessman.