"It is possible that exemption may not be effective in the marketplace," he said.
Under Dodd-Frank, the Fed is required to establish rules limiting interchange fees, which merchants pay to banks each time they swipe a customer's debit card.
Proposed rules unveiled in December would limit fees to seven to 12 cents per transaction, a 73 percent drop from the current 44-cent average.
However, in an attempt to protect smaller banks from the limits, the provision, dubbed the Durbin amendment due to the primary backing of Sen. Dick Durbin (D-Ill.), exempts financial institutions with less than $10 billion in assets from complying with the new limits.
But Bernanke warned that merchants might refuse to accept cards charging higher fees, or debit-card networks might be unwilling to handle differing fee structures for banks of varying sizes. As a result, smaller banks would have to bring their fees to comparable levels with larger institutions that must meet the new limits.
"It's possible that, in practice, they would not be exempt from the lower interchange fee," he said.
Sheila Bair, chairwoman of the Federal Deposit Insurance Corporation, said she shared Bernanke's concerns about the efficacy of the exemption.
The comments came on the same day that the House Financial Services Committee was exploring the interchange issue, hearing from stakeholders on both sides of what has been a contentious debate that pits banks against retailers.