In his court appearance, Ghosn gave a forceful rebuttal to the allegations against him, saying he has been wrongfully accused, is innocent and the accusations are merit-less.
He was then served a fresh arrest warrant on the same charge that covered the three years through March 2018.
It also alleges that he used company funds to repay a Saudi acquaintance who put up collateral for the contracts.
"We took these steps today because we believed that they are cases worthy of indictment and going to trial", said deputy chief prosecutor Shin Kukimoto. Since Ghosn's initial arrest, prosecutors have repeatedly extended his detention and re-arrested him over new allegations.
Ghosn's lawyer Motonari Ohtsuru filed a request that Ghosn be released on bail.
Ghosn had already been held in detention after being charged in November with under-reporting his income for the five years up to 2015.
"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 objective of supporting and strengthening Nissan, and helping to restore its place as one of Japan's finest and most respected companies". The judge, Yuichi Tada, said it was because he was considered a flight risk, and the possibility of concealing evidence.
The arrest and detention of Ghosn, once among the most celebrated executives in Japan, has sparked global criticism of Japan's justice system, which effectively allows suspects to be held indefinitely and questioned without a lawyer present.
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Japanese prosecutors are likely to indict him Friday, when his current detention period expires for the alleged breach of trust.
It's not uncommon in Japan for suspects to endure lengthy pre-trial detentions.
The jet-setting high-flyer who once sparked criticism for his lavish lifestyle has gone from spacious digs in global capitals to a one-man cell. He was transferred to a bigger room with a Western-style bed, according to Ohtsuru.
He has reportedly complained about the rice-based diet at the detention centre, with his family saying he has lost up to 20 kilos (44 pounds).
The Tokyo District Court on Wednesday dismissed his lawyers' request to end the detention and also rejected on Thursday their complaint filed against the decision.
The arrest of the 64-year-old has exposed rifts in the alliance he forged and led between Nissan, Mitsubishi Motors and France's Renault.
The arrest of the high-flying executive at Tokyo's Haneda airport has jolted the world's biggest auto alliance, raising questions over whether the two-decade partnership between Nissan and French partner Renault SA will survive his downfall.
Carlos Ghosn was hit with a third set of charges on Friday.
It said it took the charges filed against the firm "extremely seriously" and was continuing its investigation into the case.