Banks earned $2.8 billion in the third quarter, but nearly 40 percent of that was from a one-time accounting trick. Loan balances plummeted, and the fund that insures their deposits was $8.2 billion in the red.
The number of banks on the FDIC's "problem list" rose to 552 from 416 on June 30, the highest level in 16 years. Fifty banks failed during the quarter -- the largest number since the second quarter of 1990.
The FDIC's fund that insures bank deposits fell by $18.6 billion, mostly because $21.7 billion was set aside for expected losses on future bank failures.
The last similar deficit was in December 1991, when a predecessor fund was more than $7 billion in the red.
Separately, the Office of Thrift Supervision said Tuesday that thrifts eked out a $200 million profit in the third quarter. The agency called it "another break-even quarter," after a small second-quarter profit was revised downward to a $94 million loss.
Still, it was the first profitable quarter since the same period in 2007.
The nominal profit was $1.3 billion, but $1.1 billion was a one-time gain at a single institution. The thrift's holding company, which was not identified, shifted assets to reduce future tax expenses, agency officials said.
The agency says the number of "problem thrifts" rose to 43 from 40 last quarter.
Thrifts differ from banks in that they are required, by law, to have at least 65 percent of their lending in mortgages and other consumer loans. That makes them especially vulnerable to the housing downturn and unemployment. It also means they will play a key role in an eventual economic recovery.