However, Strunk also told the CFPB that NSF and overdraft fees accounted for 51% of credit union fee income in 2012, compared with 78% for community banks and thrifts. Large banks report a small percentage of income from NSFs and overdrafts, the report said, because they serve more large commercial accounts than do small community-based institutions.

Credit unions did get some good news in the report when comparing the amount they charge for NSFs and overdrafts. Although credit unions were categorized along with small banks, the report said small institutions charge median NSF and overdraft fees of $30, compared with $34 by the 33 largest institutions.

The report was critical of opt-in overdraft protection programs, saying that consumers who are heavy overdraft users and opted in to comply with a 2010 regulation paid $450 more during the first six months under the new rules, compared with those who did not. Opt-in users also experienced more frequent instances of involuntary account closures, which the report said makes it more difficult for the consumer to open an account in the future.

The CFPB stressed in the report that the information does not imply that banks and credit unions should be precluded from offering overdraft coverage, and in fact, the study found some progress in consumer protections.

“Nonetheless, our findings with respect to the number of consumers who are incurring heavy overdraft fees or account closures and the wide variations across institutions indicate that certain practices and procedures merit further analysis to determine whether they are causing the kind of consumer harm that the federal consumer protections laws are designed to prevent,” the CFPB said.

In a press call, CFPB Director Richard Cordray said the bureau recognizes that regulators have addressed overdraft and NSF practices in the institutions they supervise.

However, the CFPB's review intends to “help develop more consistent federal oversight of these issues across financial institutions,” Cordray said.

Cordray added that the report is just a first step in examining overdraft practices, and said the CFPB would continue to collect more data on the topic, and would act transparently should it take action.