"I have been wrongly accused and unfairly detained based on meritless and unsubstantiated accusations", the once-revered auto titan told the court.
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.
Nissan, which ousted Ghosn as chairman days after his November 19 arrest, said in a statement it remained committed to the alliance in the wake of the scandal that has strained ties with its French 43.4-percent owner.
Another member of the legal team told Reuters that they would apply for bail after Ghosn's current detention period ends on Friday, but that his release would come on Tuesday at the earliest should the court accept the application.
Ghosn's defense lawyers said they will still seek his release on bail despite the new charges. But the court rejected the request.
His lawyer said on Friday that he would make another request for bail. His detention period for the breach of trust allegations would have expired Friday if charges had not been filed.
"In general in such cases in Japan, it is indeed the case that bail is not approved before the first trial does take place", he said, adding that it could be six months before the case comes before a judge.
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.
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Ghosn, who is reportedly suffering from a fever at his Tokyo detention centre, denies any wrongdoing, arguing in a dramatic court appearance on Tuesday that he is being "wrongly accused and unfairly detained".
If proven, each of Ghosn's alleged offense may carry a sentence of as much as 10 years, prosecutors have said. Ghosn's lawyers dispute those claims.
Prosecutors say Ghosn shifted personal foreign exchange contracts with potential losses of about 16 million dollars onto Nissan. Nissan has dismissed Kelly from his role as a representative director.
Nissan and Renault stay together The legal woes have strained the partnership between Nissan and Renault, the French auto maker that owns over 40 per cent of Nissan. "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". Ghosn remains CEO of Renault.
The Renault board of directors held a special meeting Thursday night to discuss internal reviews of executive pay prompted by Ghosn's arrest.
As chairman of Nissan, Renault SA and Mitsubishi Motors Corp 7211.T , the globe-trotting Ghosn had access to a string of residences around the world, including additional homes in Beirut and Rio de Janeiro.
But Ghosn's close aide Kelly, 62, who was arrested along with the former chairman for allegedly understating remuneration, has been released on bail, while denying the allegations.