The two companies have been handling mortgages for decades
The heads of US mortgage giants Fannie Mae and Freddie Mac may each receive pay packages of up to $6m (£3.7m) for 2009, depending on company performance.
The government has put $111bn of public money into the companies since taking them over and the awards go against moves to curb lavish pay packages.
But the regulator which decided the pay levels said the awards were 40% lower than before the government bailout.
The sums involved reflected the need to attract and retain talent, it argued.
In another development, the Obama administration announced it was removing the $400bn financial cap it will provide to the two companies to keep them from failing.
Treasury department officials said the cap would be replaced with a flexible formula to ensure the companies could stand behind the billions of dollars in mortgage-backed securities they sell to investors.
'Attract and retain'
Fannie Mae and Freddie Mac play a role in funding three-quarters of all US residential mortgages.
In filings with the Securities and Exchange Commission on Thursday, the companies said Fannie Mae CEO Michael Williams and Freddie Mac CEO Charles Haldeman would each receive up to $6m, or $0.9m in salary, $3.1m in deferred payments and an additional $2m if performance targets were met.
The regulator, the Federal Housing Finance Agency, defended the size of the pay deals.
For Fannie Mae and Freddie Mac to continue to play a key role in the US mortgage market they must "attract and retain the talent needed to accomplish these objectives", said the FHFA's acting director, Edward DeMarco.
The pay deals had, he added, dropped 40% from where they stood before the companies were seized by the government and put into conservatorship in September 2008, at the peak of the credit crisis.
However, according to housing consultant Thomas Lawler, the payments are "more than what is needed for them [the CEOs] to serve their function".
"To give to someone that much to just stay on makes you question just how critical they really are," Mr Lawler, founder of Lawler Economic And Housing Consulting in Leesburg, Virginia, was quoted as saying by Reuters news agency.