The "guarantee fees" that the two government-owned companies charge would be increased in order to lessen the companies' long-term exposure to risk, said Edward DeMarco, acting director of the Federal Housing Finance Agency.

The two firms, which were seized by the government three years ago amid fears they at risk of failing, do not directly make loans. They provide financing to banks and lenders by purchasing mortgages and either keeping them on their books or packaging them for sale to investors. Those investors pay Fannie and Freddie a "guarantee fee" when they buy mortgages.

An increase in fees would be in line with the housing agency's "mandate as conservator and in terms of moving towards something that better reflects a fully private model," DeMarco told reporters after addressing a mortgage conference sponsored by the North Carolina Mortgage Bankers Association.

He said Fannie and Freddie should begin "the gradual process of increasing guarantee fees" in 2012.

Fannie and Freddie have so far cost taxpayers more than $140 billion.

The White House has backed increasing the guarantee fees as part of way to lessen the government's footprint in the U.S. housing finance system and attract more private capital to the mortgage market.

President Barack Obama included in his budget plan a recommendation for a 10 basis point increase in guarantee fees at Fannie and Freddie, which would produce projected savings of $28 billion over 10 years.

DeMarco said the changes in guarantee fees that Fannie and Freddie could charge in the coming year may include increased costs for riskier loans and for mortgages in states with more stringent foreclosure laws.

"The loss given default on a mortgage is determined in part on where that mortgage is located in the country," he said.

In October, the first step to lessen the government backstop will come when the size of the loans Fannie and Freddie, as well as the Federal Housing Administration, can purchase are set to fall back to pre-financial crisis levels.

The so-called conforming loan limit caps are set to decline from $729,500 in the highest-priced real estate markets to $625,500 on Oct. 1.

DeMarco also said the FHFA was still working on making changes to the two-year-old program that allows borrowers to refinance mortgages already owned by Fannie and Freddie. The initiative has allowed only about 830,000 homeowners to refinance, far short of its goal of reaching as many as 5 million borrowers.

"We're going back through the mechanics about how this works to see whether there are adjustments that can be made," DeMarco said. "This is something that we are looking at."

DeMarco said he is working with the Obama administration to make progress on the best way to structure a program that would convert foreclosed properties held by Fannie and Freddie into rental homes.

The goal is to shrink a glut of foreclosed properties held by the two mortgage finance giants that are weighing down the housing market and hurting home prices.