[Update 1: Adds comments from FHFA]

The Federal Housing Finance Agency is taking into consideration what government employees are paid when determining the future compensation for the CEOs at Fannie Mae and Freddie Mac.

Officials at the Inspector General’s office overseeing the FHFA confirmed the possible changes to HousingWire Wednesday. In addition, the FHFA OIG office said the regulator will be freezing salaries at the two government-sponsored enterprises in 2012.

“FHFA anticipates a substantial decrease in CEO compensation when the new CEO’s are hired,” an FHFA spokesperson said in an emailed statement, adding that there would be no cost-of-living or merit pay adjustments in 2012, the directive the agency gave last year.

Fannie CEO Michael Williams announced on Tuesday that he would step down from the post he held since 2009. He joined the company in 1991. In October, Freddie CEO Charles “Ed” Haldeman said he would resign.

Neither Williams nor Haldeman cited pay as the reason for their departures.

Tim Rood, partner and managing director of the financial advisory firm The Collingwood Group, worked under Williams at Fannie Mae for nearly six years. He doubted compensation was at the root of the reason.

“Mike has sacrificed a lot of himself for the people and the institution. I won’t speculate as to why he made the decision to step down but I highly doubt that it had much or anything to do with his compensation,” Rood said in an interview. “He is too principled and dedicated to be swayed by the threat of paycuts.”

Both men and FHFA Acting Director Edward DeMarco withstood two hearings before Congress late last year as they were grilled over executive bonuses paid in 2010. According to financial filings made more than one year ago, the top 10 employees at both firms made nearly $13 million in performance bonuses. Williams and Haldeman each made base salaries of $900,000 but received roughly $2.3 million in bonuses.

The boards for both mortgage giants are looking for CEO replacements, but DeMarco repeatedly told lawmakers during the hearings that cutting compensation for these positions would only shrink the pool of potential recruits. The GSEs, he said, need skilled people to manage the multitrillion-dollar portfolios. Another HousingWire source posits pay freezes may lead to an uptick in early retirements at the GSEs.

“There is great uncertainty for the company and its employees as we know there will be GSE reform, but we don’t know what form it will take and when,” Williams, himself, testified in November. “This uncertainty makes it very difficult to attract and retain employees with highly specialized skills, expertise, and experience.”

In a letter sent to Congress in November, DeMarco said pay levels at the GSEs were already slashed by 40%.

But lawmakers pointed out that the compensation packages were simply too high for companies that owed a combined $151 billion in bailouts as of the end of the third quarter.

The House Financial Services Committee cleared a bill that would tie GSE employee wages to those of government workers. Under the bill introduced by committee chair Spencer Bachus, R-Ala., the CEOs would have earned roughly $218,000 in 2010.

“These lavish compensation packages and bonuses are unfair, unreasonable and unjust to the taxpayers whose assistance is the only thing keeping Fannie and Freddie afloat,” Bachus said at the time.

In response to recommendations made by the Inspector General, the FHFA posted on its website the specific compensation packages GSE executives and employees at the FHFA itself received in 2010.

Spokesmen for Fannie and Freddie declined to comment.

Write to Jon Prior.

Follow him on Twitter @JonAPrior.

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