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And now, fresh off passing the 2300-page Dodd-Frank Wall Street Reform and Consumer Protection Act, Congress promises to address the “problem” of Fannie Mae and Freddie Mac.

Be afraid. Be very afraid.

Oh, not because Fannie Mae and Freddie Mac don’t need to be reformed. They sure do. They were at the heart of the U.S. housing bubble and the mortgage debacle that mutated into the global financial crisis.

And not because Congress can be counted on to compromise its way into a hash that combines the worst of private market gestures with the worst of bureaucratic rule-splitting.

No, the real danger is that a mistake in fixing Fannie and Freddie could take down the U.S. Federal Reserve. Or at least take down the Fed to the degree that any central bank, with a central bank’s ability to create money, can be taken down.

All hyperbole aside, a mistake in fixing Fannie Mae and Freddie Mac could throw the U.S. financial system into crisis again by destroying the balance sheet of the Federal Reserve.

The two entities—I don’t know quite what else to call them at the moment now that the once government agencies turned publicly traded companies turned ward of the taxpayer—played a central role in the housing bubble that led to the global financial crisis. By using an assumed government guarantee to raise cheap money from investors who persisted until the very end in thinking that so-called agency paper was “like” a U.S. Treasury, Fannie Mae and Freddie enabled mortgage lenders to pass on a riskier and riskier mix of mortgage paper to the financial markets.

And if you can pass on risk to someone else, the temptation to make more money by taking on greater and greater risk—for someone else—is almost irresistible. Certainly very few mortgage lenders were able to fight the urge. The result was shoddy underwriting that at its worst wrote mortgages to any borrower with a pulse—even if they didn’t have an income, a credit rating as high as the mortgage banker’s IQ, or any real need for the money.

Now, as a result of the mortgage debacle and the global financial crisis, private mortgage lenders from banks to savings and loans have pretty much stopped lending. In the first quarter of 2010 the two entities—plus Ginnie Mae, which had an actual explicit government guarantee before the crisis—guaranteed 95% of all mortgage originations in United States. In other words in the first quarter of 2010 Fannie Mae and Freddie Mac were the mortgage industry.

Or maybe more accurately U.S. taxpayers are the mortgage industry. The Federal government took over Fannie Mae and Freddie Mac in 2008 and taxpayers now own about 80% of the two entities.

What do we own? It’s not pretty. Fannie Mae own or guarantee almost half of the $10 trillion in outstanding U.S. mortgages. But at the end of the first quarter, Fannie and Freddie reported $330 billion in non-performing loans. And that portfolio is likely to get worse before it gets better.

In 2008, once the damage was done, both Fannie and Freddie began tightening their standards for mortgages and raised the fees they charge to guarantee bundles of mortgages wrapped up into mortgage-backed securities. For example, in 2007 10% of mortgages at Fannie and Freddie were for 95% or more of the value of the house. By 2009 that figure had dropped to just 1%

But the damage to the loan portfolios from pre-2008 lending practices is staggering. At the end of March 2010 about 4% of the mortgages originated by Freddie Mac in 2008 were delinquent by at least 90 days. For mortgages originated in 2009 the figure was a little less than 0.1%.

That’s swell—except that Fannie and Freddie guaranteed a huge number of mortgages in the boom years of 2006 and 2007. Mortgages originated in those two years make up 24% of Fannie Mae’s business, for example, but account for 67% of its credit losses,

So far, propping up Fannie Mae and Freddie Mac by providing them with the money to cover losses and stay in business has cost taxpayers $145 billion.

So far. Estimates of the total cost to taxpayers come in all over the block because they’re all based on guesses about when the U.S. economy—and the U.S. housing market—improves and how fast that improvement is. The White House estimates $160 billion. (Let’s see we’re at $145 billion and defaults are still accelerating for prime mortgages. I’ll be kind and say, Unlikely. For more on the rising number of the “best” mortgages that are now going bad see my post ) The Congressional Budget Office says $389 billion through 2019. Barclays Capital said the cost could rise to as much as $500 billion if housing prices fall by 20% from the levels of the end of 2009 and default rates triple.

If. The truth is nobody knows exactly but it’s a big figure.

And that’s really only part of the balance sheet. Taxpayers acting directly through sending truckloads of money to Fannie and Freddie were only part of the effort to prop up these entities in order to prevent the meltdown of the mortgage market and the complete collapse of housing industry.

The Federal Reserve also rode to the rescue. While taxpayers were providing billions so Fannie and Freddie could keep guaranteeing mortgages, the Federal Reserve was stepping in as a buyer to preserve at least the illusion of a market for the resulting paper. By its press release after its March 18 meeting, when the Fed began winding down its mortgage buying program, the Federal Reserve said it had The Fed, it notes in its statement, has purchased $1.25 trillion of Fannie Mae and Freddie Mac mortgage-backed securities and bought an addition $175 billion of debt from those two-entities.

Which puts the Fed’s balance sheet on the hook if anything goes wrong in the mortgage market. Or with a fix of Fannie Mae and Freddie Mac.

What could go wrong?

Normal stuff like an increase in interest rates. Remember that an increase in interest rates pushes down the price of existing bonds and other yield instruments—such as mortgage-backed securities. An interest rate increase of one percentage point would deliver a $50 billion haircut to the Fed’s Fannie Mae and Freddie Mac portfolio.

I’m not too worried about this. Not because it can’t or won’t happen but because it falls that the category of predictable bad news. The Fed has a ton of people who spend all their time worrying about the effect of interest rates on things that include the U.S. economy and, by the way, the Fed’s portfolio. The Fed may not be able to control the direction of long-term rates (the central bank only sets short-term rates) but it’s unlikely to get blindsided by the effect of interest rates on its own portfolio.

Reform—a word that covers a multitude of sins, good intentions, and botched legislation—is a far different matter. Once you start making changes in a market—and that’s what we’re talking about when we’re talking about “reforming” half of the $10 trillion in U.S mortgages—then you leave yourself side open to all kinds of unintended and unpredictable effects.

Including, and this is what worries me most, the possibility that some change will make investors lose all confidence in a market that is finally showing tiny signs of returning confidence. Remember that in the first quarter Fannie, Freddie, and Ginnie made up 95% of the mortgage guarantee market? Well, in the second quarter that figure dropped to somewhere around 85%. (I say “somewhere” because the data is not terribly reliable.) That’s not a huge change but it is progress.

What would happen if “reform” did hit the Fed’s portfolio and hit it hard? In the short term nothing much. The Fed is able to “create” money. It doesn’t face capital requirements like private banks do. Reporting and transparency standards are laughable by corporate standards.

But the long-term effects would be tremendous. At a time when the world is increasingly worried about the fiscal soundness of the United States, a major ding to the Fed’s balance sheet would further undermine U.S.  financial credibility. Overseas investors would rightly worry about the Fed managing the money supply for the benefit of its own balance sheet. I’d worry about the possibility that the Fed would manage the economy with one eye on its own balance sheet.

You can make—well, I would make—a pretty strong case, that bailing out Fannie Mae and Freddie Mac in the middle of a financial crisis and with housing prices plunging was the right thing to do. I wince when I think of sending $145 billion and counting of our money down this rat hole, but I think not doing it would have hurt too much of the economy at a time when the economy was teetering. The time to install fire alarms is before the fire. Once the building is burning, the job is to put the fire out.

And then you fix the problem that resulted in the fire.

Fannie Mae and Freddie Mac need to be fixed. More precisely they need to be dismantled. The capital markets during normal times are up to the job of setting mortgage prices (otherwise known as interest rates) and private companies can price mortgage guarantees with less distortion than entities can that feel in their heart of hearts that they can always tap the U.S. Treasury. Certainly linking that implicit guarantee with a private for profit company as Fannie Mae and Freddie Mac once were, has proven to be a really, really bad idea.

But making that fix or dismantling the two companies will require a very delicate hand on the controls. It will require setting up a mechanism for selling off the current portfolios at Fannie and Freddie without sinking the market for mortgage-backed securities and the Fed’s balance sheet. And it will require a transition period that lets private companies gradually move to provide the services to the market that Fannie Mae and Freddie Mac once did. Many countries in the world get along just fine without anything like the government participation in the housing market represented by Fannie and Freddie and they have home ownership rates comparable to the United States.

All that will require a delicate hand capable of dealing in nuances and adept at making mid-course adjustments.

Instead we have Congress.

Full disclosure: I don’t own shares of any company mentioned in this post.