There will be 1,000 more bank failures over the next two years, says BankUnited CEO John Kanas.

“We’ve already lost 81 this year,” Kanas, who became CEO of BankUnited when his private equity firm bought the bank, told CNBC.

“The numbers are climbing every day.” Many of these institutions nobody’s ever heard of. They're smaller companies.”

Kanas observes that many of these failed banks are smaller and private, which in turn exacerbates the problem for small business borrowers.

“Government money has propped up the very large institutions as a result of the stimulus package,” he notes.

“There’s really very little lifeline available for the small institutions that are suffering.”

In fact, at press time 84 banks have failed thus far in 2009, and another 416 — about 5 percent of the nation’s total banks — are on the FDIC’s “problem” list. The problem banks have a combined $299.8 billion of assets.

The numbers so far aren't nearly as bad as the 1990s crisis, when about 745 banks failed, and nowhere near Great Depression numbers, when one-third of U.S. banks collapsed during a five-year period, not to mention the hundreds of bank suspensions, temporary closings from which banks eventually recovered, that occurred during that time as well.

As financial markets heal and the economy appears to be pulling out of recession, the federal government is shifting from crisis to cleanup mode, The Wall Street Journal reports.

However, as the loss-share deals show, its potential financial burden isn’t receding.