The FDIC introduced the higher fees as called for in last year's Dodd-Frank financial reform law. The higher charge has led some companies to step out of the short-term lending markets, exacerbating an already low supply of Treasury bills used to back borrowing.

The FDIC said in a statement to Reuters that market participants were given plenty of time to consider the rule before it went into effect, and that the change may have a positive impact on credit availability as resources are directed elsewhere.