Credit unions have been raising overdraft fees on ATM withdrawals, checks and debit card purchases at a faster pace than banks to offset a decline in consumers overdrawing their accounts, research firm Moebs Services said in a report to be released Tuesday.

The report shows that banks have held the median overdraft charge at $30 a transaction for the past four years, while credit unions have upped their price from $25 to $28 a transaction in the past two years. Fees are still lower on average at credit unions as of the first three months of 2013.

“Because of changes in the payroll tax, consumers are more cautious about being hit with fees, so the volume of fee revenue has declined,” said Michael Moebs, an economist and chief executive of Moebs Services. He said overdraft revenue slipped 2.8 percent, to $31.1 billion, in the first three months of the year after a steady climb in the fourth quarter of 2012. Credit unions represent about a quarter of that revenue.

Coming out of the recession, credit unions positioned themselves as the low-fee alternative to mega-banks, which were using fee increases to offset declines in revenue. It helped that credit unions with less than $10 billion in assets were exempt from a government reduction in debit card “swipe” fees, a regulation that big banks say triggered new or higher account charges.

But credit unions have been subject to some of the other pressures that plague banks. Net interest margins — the difference between what financial institutions earn on loans and pay out on deposits — tumbled because of the low-interest-rate environment. The financial crisis has also left some credit unions battling high losses on loans. These conditions are probably contributing to the increases in overdraft fees, said Bill Hampel, chief economist at the Credit Union National Association.

Moebs said credit unions are also paying into a fund set up by the National Credit Union Administration, which regulates the industry, to cover losses on mortgage-backed securities during the downturn at certain credit unions. Those losses are projected to cost credit unions up to $15 billion.

“Credit unions have been paying for those losses for several years and are about done,” Hampel said.

Profits at federally insured credit unions topped $2.2 billion in the first quarter of 2013, slightly above the industry’s results in the last three months of 2012, according to the NCUA. Late payments and defaults on loans are also down.

By comparison, credit unions tend to offer consumers more advantageous terms on checking accounts than banks, analysts say. A recent study by showed 72 percent of credit union checking accounts remain free, compared with 39 percent at banks.

Hampel said the price credit unions charge customers for overdrawing their accounts might not reflect the actual fee income they are receiving. According to financial consulting firm Strunk & Associates, overdraft revenue accounted for 51 percent of its credit union clients’ fee income in 2012, compared with 78 percent of its community bank clients.

Moebs Services examined overdraft data from nearly 3,000 banks and credit unions. Researchers found that the largest banks have the highest price, at $35 an overdraft, while community banks and credit unions have the lowest price, $25. Financial institutions with $25 billion to $50 billion in assets reported the largest increase in fees, from $30 in 2012 to $35 in the first quarter, a 16.7 percent increase, according to the report.

The study arrives on the heels of a report from the Consumer Financial Protection Bureau that said Americans are seeing a wide variation of overdraft charges at large banks because of a patchwork of policies at financial institutions. The bureau, which focuses on banks with more than $10 billion in assets, said it plans to continue studying the issue before handing down any new rules.