TOKYO — The Securities and Exchange Commission announced Monday that it had reached a deal with Nissan to settle allegations that Nissan concealed from investors a plan to pay more than $140 million in retirement benefits to its former chairman, a scandal that led to criminal charges against the Japanese carmaker and rattled the world’s largest auto alliance.

The company will pay a $15 million fine to settle the civil fraud charges. The former chairman who was to get the undisclosed compensation package, Carlos Ghosn, agreed to pay a $1 million penalty.

The settlement is the latest fallout from the November arrest of Mr. Ghosn, who was the architect of the alliance of Nissan, Mitsubishi and Renault, on suspicion of trying to hide part of his compensation from investors and regulators. He is free on bail in Tokyo, where he faces four charges of financial wrongdoing.

The S.E.C. opened its inquiry in January in response to charges brought by Japanese prosecutors against Mr. Ghosn that he conspired with Greg Kelly, a former Nissan director, to conceal a retirement payout that was never completed. Regulators said the scheme had unfolded over a roughly nine-year period, ending only with the cases against them. Nissan itself was indicted on related charges.