They will be replaced by other Fannie Mae insiders, the Washington Post said Thursday.
The new team "will be responsible for meeting the dual objectives of conserving capital and controlling credit losses," Mudd said in a statement.
Fannie Mae and Freddie Mac are the largest source of mortgage finance across the country. Both were victims of bad bets on securities backed by home loans and badly bruised by the housing bust.
Under the shakeup, Chief Financial Officer Stephen Swad will be replaced by David C. Hisey, Fannie's senior vice president and controller.
Retiring Robert Levin is to be replaced as chief business officer by Peter Niculescu, head of the company's capital markets business, and Enrico Dallavecchia leaves as chief risk officer, replaced by Michael Shaw, a senior vice president for credit risk oversight.