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Contacted about the improperly labeled fee, BankUnited said it would investigate the matter.

"This matter is currently under review," said Mary Harris, the bank's senior vice president for marketing.

However, that BankUnited tells customers it generally calculates the fee using the same calculation as the FDIC is a big problem for the agency. It warned in the July letter that banks may be indirectly revealing information used to determine a bank's confidential supervisory ratings, something that could land them in hot water with regulators. Regulatory information is confidential to protect against bank runs and market manipulation by investors.

"In some cases some of them went into extreme detail in providing a detailed calculation of how it was done. If you give them (customers) the exact calculation ... they could determine the risk rating of the institution," James Deveney, the head of the deposit insurance section in the FDIC's division of depositor protection, said in an interview. He declined to discuss specific banks.

Under the 2010 Dodd-Frank Act, the FDIC redefined the base on which it assesses banks for deposit insurance and in April 2011 it introduced a new assessment-rate schedule for reviewing the risk factors it uses to level the deposit insurance charges. It also changed the method of pricing of deposit insurance for the largest banks - whose failure puts the entire financial system at risk - and raised its cost.

McClatchy's investigation found numerous banks in communities where it owns newspapers hitting customers with fees that sound as if they're government-mandated.

River City Bank, in California's capital city of Sacramento, boasts that it's the region's premier business bank. It charges its "FDIC Assessment" under miscellaneous fees, describing it as a variable rate applied to the average monthly ledger balance.

Contacted by McClatchy, River City's compliance manager, Tim Angello, acknowledged that the fee "appeared to be in conflict with this (FDIC) guidance" and said the matter was now under review and the fee likely to be scrapped.

"It's going to go by the wayside. There is no need to continue charging a fee that might mislead our customers," he said. "We're making the necessary changes to the fee schedules that we post online within the next few months, if not sooner."

At Columbia Bank, near Bellingham, Wash., the fee schedule includes "FDIC Insurance" at a cost of 13 cents per $1,000. City National Bank of Florida also charges a variable "Federal Deposit Insurance Corporation Assessment."

In Texas, Frost National warns of an FDIC assessment in its fee schedule, noting in a footnote that the FDIC assesses an insurance premium for all depository accounts and that its customers with the affected accounts "receive a monthly pass through allocation of the assessment for FDIC insurance based on rates set by the FDIC."

In North Carolina, Yadkin Valley Bank and Trust in the Charlotte area notes that it charges for FDIC insurance on commercial checking at a rate of 10 cents per $1,000. Bank of America doesn't charge any such deposit insurance fees, although another big Southern bank, BB&T, does so at a rate of $0.1333 per $1,000, and Georgia's Regions Bank charges a sliding FDIC fee based on ledger balances.

Capitol City Bank, which is headquartered in Atlanta, states that, "In the event of changes in the FDIC assessment set by the Federal Government, Capitol City Bank & Trust Company may increase or decrease this (FDIC Insurance) fee."

Consumer advocates were troubled by the findings of the McClatchy investigation, although not surprised. Business owners, they said, should review their bank fees and raise the issue if necessary.

"They call it an FDIC fee and they tuck it away. It's a faithful reflection of what they actually pay the FDIC, but it's never in an account holder's interest to be subjected to junk fees, and if you have a significant amount of deposits there it wouldn't hurt to point out that you are prepared to take your business elsewhere unless they eliminate it," said Joe Ridout, the manager of consumer services for the national advocacy group Consumer Action.

A revamp in 2009 of regulations that govern many consumer credit card fees, called the CARD Act, didn't affect how banks can charge fees to commercial customers, Ridout said. For credit cards and checking accounts, banks have more leeway on fees, he said.

How prevalent is the problem is of improper FDIC fees? It remains difficult to gauge because so few banks publish schedules of their fees online. It's not much better even when you walk in and ask for a schedule of fees for business accounts.

At a Bank of America branch in the nation's capital, it took several employees to dig up a hard copy of a fee schedule.

Sometimes the response to a request for a fee schedule was comical. At a branch of Capital One Bank in the nation's capital, the bank whose TV ads ask "what's in your wallet," a McClatchy reporter was provided an account disclosure form and told there was nothing else available.

That disclosure form was silent on the fees but warned potential business account customers that additional fees may apply and instructed them to "refer to a current Schedule of Fees and Charges available upon request at any of our banking offices." That's the same one that McClatchy was told was unavailable.

At a PNC Bank branch in Rehoboth Beach, Del., McClatchy was told that the fee schedule is shared only when a customer is opening an account. But at another branch of the Pittsburgh-based bank in the nation's capital, an employee printed a schedule of fees, and it didn't include an improper FDIC fee.

None of this surprises Ed Mierzwinski. He heads consumer programs for the advocacy group U.S. PIRG, an organization that since 1997 has done secret shopper tests of fee disclosures for consumer bank accounts. While unaware of any restrictions on junk fees for business accounts, Mierzwinski said banks often flouted laws, some enacted as long ago as 1991 after similarly misleading fees on consumer checking were rife, that required fee disclosure to consumers.

"Routinely, one-quarter of branches do not provide fee disclosures provided by law," he said of his group's annual secret-shopper research. "In our current research we are finding that banks sometimes put the information online, but not often. The short version is you are right: It is nearly impossible to compare bank fees, because banks make it virtually impossible to find their bank fees."

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(Kaz Komolafe of McClatchy contributed to this report.)