The 64-year-old auto tycoon was already facing charges for one allegation of under-reporting his pay, and the new charges accuse him of additional misreporting as well as "aggravated breach of trust" involving company funds.
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. His hearing at a court in Tokyo on Tuesday was his first public appearance since then.
The boards of Nissan and its French 43.4 percent owner, Renault SA, met on Thursday for an update on the Ghosn investigations, with Nissan later saying in a statement it remained committed to the alliance that has strained ties between the two automakers. Ghosn has been formally charged with under-reporting his income.
His lawyers have applied for bail, but experts say this request is very unlikely to be granted.
Otsuru earlier this week said Ghosn would likely be held until the trial which could begin in about six months.More news: AT&T will sever ties with location aggregators as well
At the end of the almost two-hour hearing, his lawyers applied for him to be freed but the court slapped this down, arguing he was a flight risk and could tamper with evidence if released.
Ghosn's detention was further extended after he was served with a third arrest warrant on December 21 for alleged aggravated breach of trust involving the transfer of personal investment losses to Nissan in 2008.
In his statement, Ghosn also listed his achievements during his time as head of Nissan, and added: "I have a genuine love and appreciation for Nissan".
The case is also being played out in local media, with another string of allegations leaking out in the Japanese press on Friday.
The Yomiuri Shimbun said $100 million from Ghosn's "CEO reserve" was paid to sales agents in 5 Middle Eastern countries.More news: Edulji Recommends Suspension for Pandya, Rahul After Legal Opinion
Ghosn's prolonged detention has put the spotlight on Japan's justice system, which has come in for some worldwide criticism.
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 has reportedly complained about the rice-based diet at the detention center, with his family saying he has lost up to 20 kilos (44 pounds). Chairman Carlos Ghosn has had a high fever since Wednesday evening and his interrogation has been suspended as a doctor said he needs rest, one of his lawyers said Thursday.
His wife Carole Ghosn said she had received no information about his health and "pleaded" with Japanese authorities for news.More news: Republicans Slam Steve King for What They Call Racist Remarks