Carfang compares FDIC premiums to the cost of buying a credit default swap on U.S. Treasury bonds, which traded around 60 basis points last week. “The cost of insuring a U.S. Treasury bond for one year was 60 basis points, yet the cost of the FDIC guaranteeing a deposit, which is basically the same thing, is only 10 basis points,” he says. “So naturally you would have a huge flow of funds out of the market and into the banking system.”

In its statement, BNY Mellon argued that the fee will eventually become unnecessary: “As markets stabilize, we expect deposit levels will trend lower as they are redeployed into the markets.”

But Carfang says that for now, many uncertainties remain. Although the debt-limit legislation has been passed, it's only a temporary fix, and treasurers still face the possibility of a U.S. downgrade and the growing debt crisis in Europe.

“We know $100 billion moved out of money market mutual funds last week, probably all into bank deposits,” he says, adding that the news of BNY Mellon's move could encourage more companies to move assets into bank deposits.

“I think the fact that BNY Mellon has gone public with their negative interest rate—they call it a fee—will cause more money to flow into the banking system,” Carfang says. “Folks are going to look at this and say, 'Wow, something doesn't smell good. Shouldn't we have our money there too?'”