The first of the two new indictments alleges that Ghosn temporarily shifted personal securities losses to Nissan, in a special breach of trust case.
Ghosn forged an unlikely three-way alliance between Mitsubishi Motors, Renault and Nissan and the board of French automaker Renault - of which Ghosn remains CEO - said late Thursday an ongoing audit into executive pay had found no sign of fraud in the last two years.
The three parties have already been indicted for understating Ghosn's income over a separate time period.
The court rejected an appeal by Ghosn's lawyers for his release from detention, and on Thursday turned down another appeal.
The charges add to an earlier charge of under-reporting his income by around half over the five years through March 2015.
The allegations relating to criminal breach of trust centre on Ghosn's handling of investment losses and payments made to a Saudi businessperson. The massive losses were generated from a contract over derivative transactions that his asset management company had concluded with a bank.
Both Ghosn and Nissan have been accused of violating Japan's Financial Instruments and Exchange Act for the misstatements submitted during the three years in question.
Motonari Otsuru confirmed that Ghosn had been indicted on the fresh allegations and said he would "shortly request his release on bail".More news: R. Kelly's attorney denies abuse allegations in documentary
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At his dramatic court appearance on Tuesday, Ghosn appeared to have lost a lot of weight in detention but otherwise seemed in good health.
"I recently learned that my husband is suffering from a high fever at the detention center in Tokyo, but my information is limited to news reports as no one in his family has been allowed to contact him since November 19", the statement by Ghosn's wife Carole said.
Renault, which is the biggest shareholder in Nissan, has refrained from removing Ghosn, instead appointing interim replacements.
Jose Munoz, widely considered as a close ally to Ghosn and a possible successor to lead the automaking partnership between Nissan and France's Renault SA, had been a "person of interest" in Nissan's widening internal investigation. Suspects in Japan are routinely held for months until trials start. Nissan has dismissed Kelly from his role as a representative director.
If proven, each of Ghosn's alleged offense may carry a sentence of as much as 10 years, prosecutors have said.
Ghosn's third arrest warrant was served on December 21 for allegedly shifting company funds to help cover his personal investment losses during the 2008 financial crisis. In a statement, Nissan said that Munoz had "elected to resign" from the company, effective immediately.
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.
"I look forward to continuing to assist Nissan in its investigations", Munoz said in the post.