Chairman Carlos Ghosn on Friday on an additional charge of aggravated breach of trust for transferring his private losses to the automaker.
Last month, he was indicted for under-reporting his income for an earlier period.
The auto executive's Japanese lawyers applied for bail soon after the new indictment on Friday.
Ghosn is being held in a cell with a toilet and a wash basin.
At a court appearance this week, Ghosn said all accusations against him were "meritless" and "unsubstantiated".
A request filed the same day by his lawyers to end his detention was rejected. The new charges claim that the under-reporting continued for three more years.
Otsuru said his team was applying for bail to have Ghosn released.
The Nikkei daily earlier reported that prosecutors planned to charge Ghosn for aggravated breach of trust on Friday.
Kelly, a Ghosn ally, was hospitalized for treatment of a pre-existing neck problem after his release and has since been discharged, said his lawyer Yoichi Kitamura.
Lawyers for the former jet-setting executive filed a bail application hours later, but have acknowledged he will probably be detained until a trial that could take months to organise. A doctor was tending to Ghosn, who has been worn down by the long detention and interrogations.
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However, in one piece of rare positive news for the once-revered tycoon, the Tokyo District Court turned down a prosecutors' bid to prevent family visits, meaning he should be allowed contact with his loved ones.
Ghosn, who has been Renault CEO since 2005, has been languishing in a Tokyo detention centre for more than 50 days as he fights multiple allegations of financial misconduct.
Ghosn, who denies the allegations, has shown no signs of backing down.
A prosecutor's office spokeswoman said the charges against Ghosn carry a maximum prison sentence of 15 years. The allegations include misrepresenting earned salary, transferring personal investment losses to the automaker, and misuse of company funds to secure credit for personal investments.
Ghosn, 64, appeared in court Tuesday for the first time since his arrest, looking thinner and grayer.
Kelly has also denied wrongdoing, saying he will restore his name in court.
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His lawyers argue that Ghosn had acted with the approval of Nissan's board and officers.
"The review process has examined the compensation of the current Groupe Renault Executive Committee members for the financial years 2017 and 2018 and has concluded that it is both in compliance with applicable laws and free from any fraud", it said in a statement.
Since his arrest, Ghosn has been removed as chairman by Nissan and Mitsubishi.
The boards of the two companies met Thursday for an update on the investigations, and Nissan later said in a statement that it remains committed to the alliance.