The Treasury Department has managed to bring in 90 cents on the dollar auctioning off stakes it held in 20 banks, but it is likely to take larger haircuts going forward as it seeks to unload its shares in some 325 banks still remaining in the Troubled Asset Relief Program.

So far this year, the Treasury has brought in $824 million of proceeds on $916 million of investments in the 20 bank holding companies and more individual auctions are planned for later this year. The Treasury's stance has essentially been that the program has made a $19 billion profits through repayments and dividend collections and it is now looking to get out.

The first 20 represented the best of the bunch, though. All were current on their dividend payments, had high capital ratios and relatively low levels of nonperforming assets, so they were not necessarily tough sells to investors. Future auctions, however, will include weaker banks that are still struggling with credit issues and, in many cases, have deferred quarterly dividend payments to the Treasury in order to preserve capital.

"The Treasury got rid of some of the best ones first. They all give investors reasons to believe that with sufficient time they would repay in full," said Rob Klingler, a partner at Bryan Cave. "As you move down the list, the asset quality is not as good and that is likely going to be reflected in the pricing. The investors want to know when they are going to get their principal back."

The Treasury declined to comment for this story, but past statements by agency officials indicate that it is prepared for bigger discounts going forward.

"We have already estimated that the value of these investments is less than par in our budget projections, and we'll only sell above a pre-set reserve price in order to best protect taxpayer value," Timothy G. Massad, assistant secretary for Financial Stability at the Treasury, wrote in a May blog post about the winding down of Tarp.

The small size and private structure of many of the remaining banks could also widen the discount, said Joshua Siegel, the chief executive of StoneCastle Partners, a New York fund that invests in community banks.

"Going forward, most of the remaining banks are non-public or don't have much public research. Are institutional investors willing to pay the same yield for a small bank as they would for a big bank?" Siegel said. "You have to think the discount increases, but by how much? There is no way to know what the appetite will be for illiquid perpetual issuances from private institutions."

Still, Bryan Cave's Klingler said that while the quality of the remaining banks might not be as good, prices could still be lifted by the limited supply - and potential return to investors. Banks are currently paying a dividend of 5%, but those that have yet to repay Tarp in full by late 2013 or early 2014 will see their dividend payments jump to 9%.

"In this environment, there is significant demand for an investment with a fixed return of 5% and 9%. That is better than you can get just about anywhere," Klingler said. From that standpoint, the prices the Treasury fetches at future auctions "may reflect smaller discounts going forward."

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