Ghosn has been arrested on suspicion of breaching the Financial Instruments and Exchange Act by stating only 5 billion yen ($44 million) of his 10 billion yen compensation during the five years through March 2015 in Nissan's securities reports submitted to Japanese regulators.
Authorities then re-arrested him later Monday over separate allegations that he also under-reported his income by a further four billion over the past three years.
Some kind of action by the prosecutors had been expected, because the detention period allowed for the allegations in question was set to end by close of business on Monday.
"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 company said in its statement.
If confirmed, it would represent another blow to the company, which has been rocked since Ghosn was arrested on November 19 on allegations he underreported his salary by millions of dollars over five years.
Executives are suspicious of Nissan's motives, demanding to see proof from the Japanese carmaker of the accusations against Ghosn, people familiar with the matter have said. "Nissan will continue its efforts to strengthen its governance and compliance, including making accurate disclosures of corporate information".
While Nissan itself was also charged in court on the initial allegations, the company was not mentioned in the latest allegations.
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The vehicle company itself has also been charged - accused of making false statements in annual reports - according to the reports.
Tension within the Franco-Japanese partnership that has been held together by Ghosn for two decades has all but exploded into the open since his shock incarceration.
Nissan on Friday announced plans to recall approximately 150,000 vehicles owing to improper tests on new units, dealing a fresh blow to the Japanese auto giant following the shock arrest of former chairman Carlos Ghosn.
He has reportedly told embassy visitors he is being well treated but has complained of the cold, with Monday's temperature in the Japanese capital hovering around five degrees Celsius.
If found guilty, Ghosn could face a 10-year prison sentence.
He spends his time reading books and news reports and is said to be unhappy about the rice-based food.
The prosecutors believe the payments were fixed as they have obtained documents on his post-retirement compensation signed by Ghosn.
He is thought to have deferring part of his pay to avoid criticism of his high salary from employees and shareholders. A commission official said Monday that Nissan, Ghosn and Kelly were suspected of falsifying reports on millions of dollars' worth of Ghosn's income.