This is the fourth indictment against the former boss of the Nissan-Renault auto alliance.
The charges filed on Monday are related to payments by a subsidiary of Nissan that allegedly went to a private investment company controlled by Ghosn.
Ghosn, 65-years-old, has always claimed he is innocent of all financial misconduct charges against him. He was first arrested in November, then secured a release in March after paying 1 billion yen (approximately 8 million euros). Then he was later re-arrested on April 4.
Monday was the end of the maximum period authorities had to question Ghosn who is not technically in pre-trial detention.
Japan's justice system allows authorities to keep suspects in custody for prolonged periods.
Nissan said on Monday that it had filed a criminal complaint against Ghosn related to the indictment.
The company determined that the payments in question "were in fact directed by Ghosn for his personal enrichment and were not necessary from a business standpoint."
The Tokyo District Prosecutors' Office said in a statement that Ghosn caused around 4 million euros ($5m) in financial damages to Nissan by siphoning off half of 9 million euros ($10m) that he had a Nissan Motor Co. subsidiary transfer to an overseas sales agent for the automaker in 2017 and 2018.
The indictment alleges that Ghosn diverted over two million euros in July 2017 and another 2 million euros in 2018 from the sales agent to his private investment company for his personal benefit.
Tokyo deputy-chief prosecutor, Shin Kukimoto, said on Monday that his team has gathered "enough evidence to win convictions in all four counts of charges."
Ghosn' wife, Carole, has also been questioned by prosecutors in Tokyo. She has been very active in attemptong to rally support for her husband.
She has flown to France to ask the government to intervene in the case and appeared in multiple media interviews in the United States where she has repeatedly proclaimed her husband’s innocence.