WASHINGTON, DC-A new report by the Treasury Department shows what other earlier data has suggested: small banks are in trouble. This particular data point comes from a May report to Congress on the status of TARP repayments. It found that 101 bailed-out banks that participated in the program have missed paying the government a dividend. Nearly all of these banks are small institutions. That 101 figure is a 25% increase from February.

On the whole, the program is doing well, according to the report, which also said that the total amount repaid by banks to the program has surpassed the amount of outstanding debt for the first time. In May, total repayments reached $194 billion, while the outstanding debt is $190 billion. There are some caveats to this milestone, however. Namely, the outstanding debt amount does not include $106 billion that has been committed to institutions but has yet to be paid out. With that added to the final tally, the outstanding debt becomes $296 billion.

The news about the small banks is especially disconcerting, though, coming on the heels of other indications that these institutions--most of which are burdened with sour real estate loans--are not regaining their financial health as quickly as their larger counterparts.

In February, a Congressional Oversight Panel sounded the alarm over banks' vulnerability to falling commercial real estate values and the trouble many owners will have in refinancing debt that is coming due. The agency cited figures that have become routine knowledge within the industry: between 2010 and 2014, about $1.4 trillion in commercial real estate loans will reach the end of their terms. Nearly half are underwater as commercial property values have fallen more than 40% since the beginning of 2007.

Increased vacancy rates continue to exert a powerful downward pressure on the value of commercial properties. It will be the smaller regional and community banks--which have higher concentrations of such loans--that will experience a disproportionate share of defaults, compared to larger national or money center banks, the report found.

Small banks--and jumpstarting lending to these companies, including for real estate purchases--have been a focus of the Obama Administration, which has been pressing Congress in recent weeks to pass its $30 billion aid package to small businesses.