The report also says the top 333 of those managers are vice presidents who had median pay of $388,000. That's close to salaries paid by private financial firms and exceeds pay for similar jobs at federal agencies.
Because the FHFA doesn't closely evaluate the compensation of senior managers, it is unable "to ensure that the costs associated with senior professional compensation are warranted," the report says.
The FHFA said Monday that it agreed with the inspector general's conclusion that it should improve its oversight of senior managers' pay. The FHFA said it plans to make a full review.
Taxpayers so far have paid roughly $170 billion to rescue Fannie and Freddie, which suffered huge losses from risky mortgages during the 2008 financial crisis.
Under pressure from Congress, the FHFA earlier this year capped pay for Fannie and Freddie's CEOs at $500,000 a year. The agency also cut pay for about 50 other executives, who were earning more than the companies' senior managers looked at in the latest report.
In December 2010, the agency imposed a freeze on merit pay increases and cost of living adjustments for all Fannie and Freddie employees in 2011. It later was extended to cover 2012.
The agency and the two companies have said that the relatively high levels of compensation are needed to attract and keep qualified employees.
"There's a lot at stake for our country and it is absolutely critical that Fannie Mae compensation is competitive in the market for financial services talent," Fannie spokeswoman Kelli Parsons said in a statement Monday.
Compensation for Fannie employees has declined "substantially" from the levels of pay before the government takeover, Parsons said.
Spokesmen for Freddie had no immediate comment.
