In an attempt to boost its dwindling reserve fund, the FDIC -- the organization responsible for insuring deposits and taking over failed banks -- is changing how it'll charge a one-time special assessment free to member banks. The new rule shifts much of the cost from traditional commercial banks to old Wall Street banks that didn't rely on deposits to fund their balance sheets.

Under an old proposal, the FDIC planned on charging banks a one-time special $0.20 fee per every $100 in deposits. Now, banks will be charged $0.05 for every $100 in total assets less Tier 1 capital. Since big banks often have much more total assets than they do deposits, the new method shifts the burden from small banks to some big banks.

Here's how the deposit and asset makeup of the six largest banks looks:

Bank

Total Deposits

Total Assets Less
Tier 1 Capital

Citigroup (NYSE:C)

$763 billion

$1.7 trillion

Bank of America (NYSE:BAC)

$954 billion

$2.2 trillion

JPMorgan Chase (NYSE:JPM)

$907 billion

$1.9 trillion

Wells Fargo (NYSE:WFC)

$797 billion

$1.2 trillion

Goldman Sachs (NYSE:GS)

$45 billion

$864 billion

Morgan Stanley (NYSE:MS)

$60 billion

$578 billion

The new fees will only adversely affect Goldman Sachs and Morgan Stanley -- the other, deposit-heavy banks in the table are actually better off. Both opted to become bank holding companies last fall after AIG (NYSE:AIG) blew up, subjecting themselves to FDIC oversight. Now that they want to be lumped in with the commercial banking crowd, they're going to have to pay a hefty fee to make up for others' past mistakes.

Which, frankly, they should. Being a bank holding company gives these banks -- which have a negligible reliance on deposits -- a tremendous safety net. It's entirely unfair for smaller banks to pay a proportionally larger share over larger banks for what are essentially the same benefits.

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Fool contributor Morgan Housel doesn't own shares in any of the companies mentioned in this article. The Fool has a disclosure policy.