The U.S. government seized control of the mortgage giants Fannie Mae (FNM) and Freddie Mac (FRE) on Sunday, placing the liabilities of more than $5 trillion of mortgages onto the backs of the U.S. taxpayer.

Both companies have now been placed into a government conservatorship under the recently created Federal Housing Finance Agency, in a plan announced by Treasury Secretary Henry Paulson and FHFA Director Jim Lockhart.

The chief executives of the mortgage companies – Dick Syron of Freddie Mac and Daniel Mudd of Fannie Mae – have stepped down, but will continue to stay on temporarily to oversee the transition, Paulson said. Herb Allison, former chairman of TIAA-CREF, will take over as CEO of Fannie, while U.S. Bancorp (USB) Chief Executive David Moffett will become CEO of Freddie.

"Fannie Mae and Freddie Mac are so large and so interwoven in our financial system that a failure of either of them would cause great turmoil in our financial markets here at home and around the globe," Paulson said, speaking at a press conference in Washington D.C. on Sunday morning. "A failure would affect the ability of Americans to get home loans, auto loans and other consumer credit and business finance."

The Sunday announcement and themes of "too big to fail" brought stark reminders of the government's March intervention in the case of Bear Stearns, which came within hours of filing for bankruptcy.

It also brings both Fannie Mae, which was created by Congress during the Great Depression to help with home ownership, and Freddie Mac, created in 1970 as a competitor to Fannie Mae, back into the fold of the government after a multi-decade attempt at privatization.

As part of the plan, both Fannie's and Freddie's day-to-day operations will be under the direction of Lockhart. Officials provided no indication of when the government conservatorship will end. That will depend partially on the health of the U.S. housing economy, as well as the policy choices of the next presidential administration.

"Conservatorship will give the enterprises time to restore the balances between safety and soundness and provide affordable housing and stability and liquidity to the mortgage markets," Lockhart said.

As part of the government's plan to take over the companies, and to protect taxpayers, Paulson said the Treasury will receive $1 billion in senior preferred stock, with a yield of 10% a year, in both Fannie and Freddie, and will also receive "warrant for the purchase of common stock of each company representing 79.9% of the common stock of each company on a fully diluted basis at a nominal price."

The government's plan will all but wipe out any value that common or preferred stockholders have in the two mortgage companies. All dividends for Fannie and Freddie will be eliminated, Paulson said.

All political lobbying efforts by the government-sponsored entities will cease as well.

While under the direction of the government, the two companies will take additional mortgage-backed securities to help stabilize the mortgage markets through the end of 2009, Paulson said. Starting in 2010, when the housing market is expected to be recovering, both Fannie and Freddie will reduce the size of their mortgage portfolios at a rate of 10% a year.

The ultimate goal is to reduce the size of Fannie and Freddie's mortgage holdings -- around $1.5 trillion altogether -- to about $250 billion each.

Because the government controls the liabilities of Fannie and Freddie, this action could cost U.S. taxpayers billions of dollars. However, Paulson emphasized that, because of the long-term value of these securities, the taxpayer would have "a large stake in the future value of these entities."

"The ultimate cost to the taxpayer will depend on the business results of (Fannie and Freddie) going forward," Paulson said.

The action was endorsed and planned in cooperation with the Federal Reserve and Congress, including House Financial Services Committee Chairman Rep. Barney Frank, D-Mass.

"These necessary steps will help to strengthen the U.S. housing market and promote stability in our financial markets," said Fed Chairman Ben Bernanke in a statement.

Ratings agency Standard & Poor's affirmed Fannie's and Freddie's long-term AAA credit rating.

"We believe the government has now clearly reinforced its support of (Fannie and Freddie)," said S&P credit analyst Victoria Wagner, in a statement.

Democratic Presidential Candidate Sen. Barack Obama, D-Ill., said "given the substantial role that Fannie Mae and Freddie Mac play in our housing system, I believe that some form of intervention is necessary to prevent a larger and deeper crisis throughout the entire economy."

The implications to consumers and taxpayers are not immediately clear. Unlike the bailout of Chrysler in the early 1980s or the airlines after the Sept. 11, 2001, terrorist attacks, where the amount of money loaned to corporate America was clear, the U.S. government could be on the hook for losses for years into the future. Paulson could not provide an estimate of how much the plan would cost taxpayers.

Mortgage rates are expected to be unaffected in the short term.