Former Nissan chairman Carlos Ghosn, another executive and the carmaker itself have been charged by prosecutors in Tokyo with under-reporting income.
The charges imposed on Monday involve allegations Ghosn's pay was under-reported by about five billion yen (£34million) over five years.
The prosecutors had said earlier that the allegations were behind Ghosn's November 19 arrest.
They added a new set of allegations on Monday against Ghosn and another executive, Greg Kelly, of under-reporting another four billion yen (£28 million) for more recent years.
Nissan as a company was not mentioned in the latest allegations.
In Japan, a company can be charged with wrongdoing.
Some kind of action by the prosecutors had been expected because the detention period allowed for the allegations disclosed earlier was to end on Monday.
Kelly, 62, is suspected of having collaborated with Ghosn.
Kelly's lawyer in the US said he is asserting his innocence.
Ghosn has not commented.
He has been ousted as Nissan chairman and Kelly lost his representative director title following their arrests, but they both remain on the board.
Ghosn, 64, was sent to Nissan by its partner Renault SA of France in 1999 and led a dramatic turnaround of the near-bankrupt Japanese carmaker.
But Ghosn's star-level pay drew attention since executives in Japan tend to be paid far less than their international counterparts.
Only Ghosn's lawyers and embassy officials from Lebanon, France and Brazil, where he has citizenship, have been allowed to visit him.
Nissan said in a statement: "Nissan takes this situation extremely seriously. Making false disclosures in annual securities reports greatly harms the integrity of Nissan's public disclosures in the securities markets, and the company expresses its deepest regret."
The statement said Nissan would work to improve its corporate governance and compliance, "including making accurate disclosures of corporate information".
Meanwhile, the Securities and Exchange Commission said it had filed criminal complaints against Ghosn, Nissan and Kelly.
A commission official said on Monday that Nissan, Ghosn and Kelly were suspected of falsifying reports on millions of dollars' worth of Ghosn's income.