The watchdog said the former car giant boss and subordinates deceived Nissan and its investors – including in the US – in not declaring the payment scheme in company accounts.
Mr Ghosn also agreed to a 10-year ban on being a director in the US.
The Securities and Exchange Commission filed the settled charges on Monday against Nissan, Mr Ghosn, and former director Greg Kelly, accused of aiding and abetting the former boss.
According to the SEC’s orders and complaint, the Nissan board delegated authority to Mr Ghosn from 2004 to set individual director and executive compensation levels, including his own.
It charged the Japanese auto giant with violating the anti-fraud provisions of the Securities Exchange Act.
Nissan settled the charges, agreeing to pay a $15m (£12m) penalty and to cease and desist from committing or causing violations of the anti-fraud provisions.
Mr Kelly agreed to a $100,000 penalty, a five-year director ban and five-year suspension from practising or appearing before the commission as an attorney.
None of the charged admitted to any wrongdoing.
The US financial regulator said: “From 2009 until his arrest in Tokyo in November 2018, Ghosn, with substantial assistance from Kelly and subordinates at Nissan, engaged in a scheme to conceal more than $90m of compensation from public disclosure, while also taking steps to increase Ghosn’s retirement allowance by more than $50m.
“Each year, Ghosn fixed a total amount of compensation for himself, with a certain amount paid and disclosed and an additional amount that was unpaid and undisclosed.”
The SEC added that Mr Ghosn and staff including Mr Kelly, created various means of structuring payment of the undisclosed retirement compensation, such as entering into secret contracts, backdating letters to grant Mr Ghosn interests in Nissan’s long term incentive plan.
They also changed the calculation of Ghosn’s pension allowance to provide more than $50m in additional benefits
They misled Nissan’s finance chief, and the company issued a “misleading disclosure” relating to the increased pension allowance, the SEC said.
Steven Peikin, co-director of the SEC’s division of enforcement said: “Through these disclosures, Nissan advanced Ghosn and Kelly’s deceptions and misled investors, including US investors.”
“Investors are entitled to know how, and how much, a company compensates its top executives.
“Ghosn and Kelly went to great lengths to conceal this information from investors and the market.”