The Securities and Exchange Commission filed the charges in Manhattan against former Federal Home Loan Mortgage Corp. Chief Executive Officer Richard Syron and two other former Freddie Mac executives, Patricia and Donald Bisenius.
Similar charges were filed against Federal National Mortgage Association CEO Daniel Mudd, former Fannie Mae Chief Risk Officer Enrico Dallavecchia and Executive Vice President Thomas Lund, The New York Times reported Friday.
"Fannie Mae and Freddie Mac executives told the world that their subprime exposure was substantially smaller than it really was," said Robert Khuzami, director of the SEC's Enforcement Division.
"These material misstatements occurred during a time of acute investor interest in financial institutions' exposure to subprime loans, and misled the market about the amount of risk on the company's books," he said.
The two banks are considered government-supported enterprises, as they accept the role of buying mortgages from banks to encourage more lending and expanding homeownership.
The banks were encouraged to do so by the government and by banks that did business with Fannie Mae and Freddie Mac.
By 2005, the two companies attempted to increase their share of subprime mortgages, as Wall Street was going through a housing boom -- more accurately a mortgage boom.
By 2008, however, the market had soured and banks had billions of dollars worth of frozen assets on their books.
The government has since loaned Freddie Mac and Fannie Mae more than $100 billion to keep them afloat, The New York Times reported.
The Obama administration has already said it would unwind the two banks, the Times said.