The rating agency says in a report Thursday that the loss-soaked mortgage companies may still be taking their lumps on bubble-era mortgages in 2012.

Fannie and Freddie have already set aside tens of billions of dollars to absorb mortgage losses, and loans aren’t going to sour as rapidly as they did a year or two ago.

But the quality of their assets “continues to worsen,” S&P notes, thanks to a weak economy and glutted housing market. And resolving troubled loans is taking longer, because of the sheer volume of foreclosures and the complications of the loan modification process.

“While Fannie and Freddie are adding quality new business, they are working out significant amounts of troubled loans that could take three or more years to clear from the weakest 2006-2008 vintages,” analysts Daniel Teclaw and Vandana Sharma write in their first-quarter update.  “Actual recognition of significant losses could occur as late as 2012, or later, for the 2008 vintage.”

The companies’ parlous condition is no secret, of course. Fannie and Freddie have received $145 billion of taxpayer support since they were seized by the government in 2008, and Fannie said last month that it expected to keep losing money for the “indefinite future.”

The firms’ regulator, the Federal Housing Finance Agency, said in its annual report to Congress two weeks ago that Fannie and Freddie “each remain critical supervisory concerns,” due to a weak housing market, the ongoing foreclosure crisis and questions about their systems and risk management.

Because of the government’s essentially unlimited support for the mortgage market, even additional losses won’t necessarily drive up the companies’ ultra-low borrowing costs. They will continue to enjoy federal support at least through 2012, following the government’s Christmas Eve decision to vastly expand the scope of the safety net being provided to the companies.

Fannie and Freddie financed 76% of single-family mortgages issued last year, the FHFA said, and policymakers fear that any sign of weakening support for them could disrupt the housing markets.

But with investors around the world grappling with the risks of burdensome government debt loads, the federally funded status quo may be more fragile than it appears.

“To date, the Obama administration has not pressed forward with any GSE alternative strategies, even as part of the ongoing regulatory reform discussions,” S&P writes, referring to Fannie and Freddie’s status as government-sponsored enterprises. “In our view, however, any dramatic changes in policy that signal less support for the GSEs will be a negative factor for the supported rating.”