CEOs of financial institutions received an average 1 percent increase in total cash compensation in the past year, the lowest level in three years, according to a survey by accounting firm Crowe Horwath.

That was down considerably from the 4.7 percent increase the CEOs enjoyed in 2008. The survey of 320 U.S. financial institutions found that base salaries for all financial institution positions increased an average of 2.2 percent in 2009 despite the financial crisis.

According to Timothy Reimink, a senior consultant in Crowe’s performance group, the small increase in total compensation for CEOs masks a trend: In recent years, base salaries for CEOs have increased at rates faster than most other employees, while bonuses as a percentage of salary have declined. This year, independent bank CEOs received an average of $260,047 in total compensation.

In addition to CEOs, several other job titles at financial institutions experienced either no growth or decreases in compensation for the same one-year period. Chief credit managers saw their compensation shrink by 6.4 percent, branch managers saw a decrease of 5.8 percent, and commercial loan officers saw no increase in compensation. According to Reimink, this trend in total compensation is partly due to the decline of bonuses in recent years.

On the other end of the spectrum, overall compensation increased during 2009 nearly 20 percent for loan workout officers, 13.9 percent for top retail banking officers, 12.4 percent for top human resource officers, and 10 percent for top loan managers.

In 2009, chief internal auditors for financial institutions saw an increase of 8 percent in their average compensation. According to Reimink, above-average compensation increases for the position most responsible for ensuring compliance is likely to continue during this time of heightened scrutiny.