By enlisting Fannie Mae (FNM) and Freddie Mac (FRE) in its dramatic fight against the foreclosure crisis, the Obama administration is boosting the importance of the two troubled mortgage entities while also increasing the risk that the firms will continue to lose money.

The move, announced as part of a broad package of housing, mortgage and foreclosure proposals, is winning the applause of some experts while others remain concerned about the long-term impact on the mortgage finance giants.

Under the plan the administration unveiled Wednesday, Fannie Mae and Freddie Mac would refinance loans in effort to make mortgages more affordable for as many as 4 million to 5 million homeowners who are unable to refinance because of plummeting home prices. The centerpiece initiative would be limited to borrowers who took out a conforming loan owned or guaranteed by one of the two government-sponsored enterprises and would allow them to refinance even if they owe more than 80% on the value of their home.

At the same time, the Treasury Department agreed to boost its funding commitment to Fannie and Freddie - which were seized by the government in September amid concerns they would collapse from mounting mortgage defaults - to $200 billion each from the original level of $100 billion each.

"Fannie Mae and Freddie Mac are critical to the functioning of the housing finance system in this country and play a key role in making mortgage rates affordable and maintaining the stability and liquidity of our mortgage market," Treasury Secretary Timothy Geithner said in a statement Wednesday morning.

New America Foundation Financial Services Policy Director and former Clinton administration economic policy official Ellen Seidman said the administration is right to lean on Fannie and Freddie to ease the pain in the housing markets.

"I think it's exactly the right thing to do," she said in a phone interview. "You now have these two pretty well-oiled machines. We've essentially nationalized them, so let's use them."

Seidman, who also serves as a top executive for Chicago-based community development bank ShoreBank Corp., added that the homeownership plan would go a long way to help ShoreBank boost lending to homebuyers.

Still, some experts point out that the mortgage market has already dealt a blow to Fannie and Freddie. They worry that the firms' new refinancing role will only lead to substantially more losses for the government-sponsored enterprises, or GSEs.

"They [the GSEs] will become deeper in the hole financially as they get further into this mortgage modification business ... but we don't get any sense whatsoever of what happens to them," said banking industry and monetary policy consultant Bert Ely. "It exacerbates the longer-term question which is what is the future of Fannie and Freddie."

Treasury's decision to boost funding to $200 billion each for the government-sponsored firms is a move to ease investors' concerns about the GSEs' role in the housing plan, given that GSE debt carries only an implicit government guarantee, Ely said.

"This is the government's way of saying to the owners of Fannie and Freddie bonds and mortgage-backed securities: 'You're protected. We're going to put some money in, therefore, you don't have to worry about getting repaid,'" Ely said.

Still, Ely said the more Fannie and Freddie get drawn into the shaky mortgage market, the harder it is going to be for policymakers to address issues about the firms' fate. Once the GSEs were placed under government control, policymakers began debating what form the firms should take to resolve conflicts in their hybrid structure. Former Treasury Secretary Henry Paulson, for instance, proposed that the GSEs be recast into a public utility model through which the companies would be replaced by one or two private firms subject to regulation by a commission that would limit their profitability.

FTN Financial agency debt analyst Jim Vogel also said the GSE funding hike is a clear sign that the government understands the markets will be sensitive to the potential cost of increased homeownership assistance. "The administration couldn't accomplish its housing goals while raising doubts about existing GSE securities," he said.

Still, very few experts were surprised that the Obama administration put the GSEs front and center in its housing plan, partly because government officials are having to be creative when it comes to financing rescue efforts.

"It's not surprising to me that so much of the plan revolves around Fannie and Freddie because there's a limited amount of money in the [Treasury's Troubled Asset Relief Program]," said Robert Litan, a senior fellow at Brookings Institution. He applauded the administration for employing the GSEs in an effort "to change the rules on refinancing," but noted that his support is unlikely to be universal.

"I know there are going to be critics," he said. "This is basically asking Fannie and Freddie to dig a deeper grave."

However, the housing crisis is in need of a very aggressive, targeted effort to stem foreclosures and it makes sense to use the GSEs to make mortgages more affordable for more homeowners, Litan said.

"Virtually every economist from the right or the left or the middle has said you're not going to fully solve the banking problem unless you do something about housing," he said. "You may be causing deeper losses for Fannie and Freddie but you're saving yourself on the other side from having to bail out the banks so much."

Similarly, American Enterprise Institute fellow and former White House counsel to President Ronald Reagan Peter Wallison said he agrees with the Obama administration's decision to rely heavily on Fannie and Freddie for its housing fix.

"Now that they have been taken over by the government, they should be used to the maximum extent possible to address the mortgage problem," Wallison said. "They were always the best institutions for doing that and the fact they own so many mortgages or control so many pools of mortgages ... it makes a tremendous amount of sense to do that."

However, Wallison echoed Ely's comments when it comes to questions about the impact the housing plan will have on the GSEs over the longer-term.

"They're no longer being treated as private companies of course. They're doing things the government wants them to do - not for profit," Wallison said. "That's good, but it does create some difficult problems at the end of the line when they have to deal with shareholders. That'll be a real puzzle."

-By Maya Jackson Randall, Dow Jones Newswires; 202-862-9255; maya.jackson-randall@dowjones.com

(Michael Crittenden and Jessica Holzer contributed to this report.) -0-