The decision at the Tokyo District Court means the 64-year-old auto tycoon is likely to stay in custody until his trial, which even his own defence lawyer has admitted could take six months to begin.
Ghosn's main defence lawyer Motonari Otsuru immediately vowed to appeal the court decision.
On Friday, prosecutors pressed formal charges against Ghosn over two more allegations of financial misconduct -- all of which the Franco-Brazilian-Lebanese businessman denies.
In a dramatic courtroom appearance on Tuesday, Ghosn denounced the allegations against him, saying he had been "wrongly accused and unfairly detained".
He has been indicted on two counts of allegedly under-declaring his income by more than nine billion yen in total over eight fiscal years in documents to shareholders.
Japan's legal system under international criticism
Ghosn also stands charged with "aggravated breach of trust" over a complex alleged scheme in which he is said to have tried to transfer foreign exchange losses to Nissan's books.
His ongoing detention has prompted some international criticism of Japan's legal system, which permits prosecutors to hold suspects while they investigate an allegation, and also allows lengthy pre-trial detention once charges have been filed.
Carole Ghosn, his wife, has alleged her husband is being held in "harsh" conditions and subjected to round-the-clock interrogations intended to extract a confession.
His arrest has exposed rifts in the alliance he forged and led between Nissan, Mitsubishi Motors and Renault.
While the 2 Japanese firms quickly ousted him from his leadership roles, Renault has kept him on and its board said on Thursday that an ongoing audit has found no sign of fraud in the last two years.