When Fortress Investment Group hired Daniel Mudd, the former chief executive of Fannie Mae, as its chief executive in 2009, the asset manager knew that the government investigations into the mortgage company clouded the hire.

On Friday, those clouds darkened after the Securities and Exchange Commission charged Mr. Mudd with securities fraud for allegedly understating Fannie’s exposure to subprime mortgages. The commission also sued two other Fannie executives and three former officials at Freddie Mac.

“This morning, the SEC filed a civil complaint against Dan Mudd, related to matters associated with his previous employment at Fannie Mae,” said Gordon Runte, a Fortress spokesman. “The complaint does not relate to Fortress, and this matter has not impacted our company or our business operations. We are undertaking a thorough review of the matters addressed in the complaint.”

Mr. Mudd denied the charges, issuing a statement through his lawyer, Jamie Wareham.

“Every piece of material data about loans held by Fannie Mae was known to the United States government and to the investing public,” said Mr. Mudd. “The S.E.C. is wrong, and I look forward to a court where fairness and reason — not politics — is the standard for justice.”

While the civil charges have nothing to do with Mr. Mudd’s conduct at Fortress, corporate governance experts say that company’s directors have a difficult decision about whether to keep him at the helm. When the S.E.C. warned him earlier this year that it could file charges, Fortress’s board stood behind him.

“There is no rule requiring him to step down, but it’s a complicated situation,” said Jill E. Fisch, a professor of corporate law at the University of Pennsylvania Law School.

“The board has to ask themselves whether this is a problem in terms of his integrity,” she said. “Plus, there’s the negative public relations associated with the case and the distraction of having to deal with the charges.”

Fortress hired Mr. Mudd in July 2009, nearly a year after the government forced him out as Fannie’s C.E.O. He succeeded Wesley Edens, the co-founder of Fortress and its largest shareholder. Bringing on Mr. Mudd freed up Mr. Edens and his top executives to focus on their private equity portfolios and hedge funds, which had been buffeted by the global financial crisis.

New York-based Fortress was started in 1998 by five former executives of Lehman Brothers and Goldman Sachs. It benefited from the industry’s extraordinary growth over the past decade, and was the first large so-called alternative asset manager to sell its shares to the public. Its early 2007 I.P.O., and the sale of a minority stake to Nomura Holdings just prior to its offering, made Fortress’s founders hundreds of millions of dollars.

Today, Fortress manages about $44 billion in assets. While the firm has recovered from the sharp downturn, several of its businesses have continued to struggle, including weak performance in a “global macro” hedge fund that places bets on a range of investments around the globe, from U.S. stocks to Asian currencies.

The company’s stock performance also continues to sag. On Friday afternoon, shares stood at $3.40, nearly the exact price that it traded at on the day the company announced Mr. Mudd’s appointment.

Mr. Mudd, 52, is the son of Roger Mudd, the former television journalist. Earlier this month, at a Goldman Sachs investment conference, the Fortress chief spoke about the challenges facing Europe’s economies and, more broadly, the political and regulatory uncertainty around the world.

“This is no joyful state of affairs for us as human beings, but it is actually a very good investment environment,” he said. “Maybe the best we’ve seen in our lifetime.”