Senior public servants' salaries increased at almost twice the rate of their staff's pay rises last year.
The federal bureaucracy's latest pay-tracking data, released on Wednesday, shows remuneration continued to grow moderately after several years of stagnation following the Coalition's 2013 election win.
The median base salary for APS and executive-level staff rose 2 per cent, while senior executive service salaries increased by 3.8 per cent, the fastest annual growth in five years.
Under the Coalition's current wage-bargaining policy, government agencies are limited to offering junior and mid-level public servants pay rises of 2 per cent a year.
However, most SES staff are employed on individual contracts rather than collective agreements.
The Public Service Commission said several factors influenced the latest increase in SES salaries.
"These include movements between agencies, differences in remuneration policy by agency and the creation of new SES positions, and an apparent move to roll motor vehicle-related allowances into base salary for some employees," the commission's report said.
The typical federal bureaucrat in Canberra - an executive level 1 officer - had a base salary of $113,866 on December 31, 2018. The median APS level 6 employee's salary was $91,238.
Total remuneration - an amount that includes allowances, superannuation, bonuses and other benefits - increased more modestly across the Australian Public Service.
Non-SES staff's median total pay rose 1.5 per cent, while SES median total pay increased by 1.4 per cent.
This was partly due to reduced use of performance bonuses. The report said the overall number of staff who received these bonuses had fallen by 33 per cent since 2014.
Only one in every 21 SES officers received such a bonus last year, it said.
"The data suggests that although the overall number of employees receiving performance bonuses has continued to decrease in 2018, the average value of those bonuses has increased."
Meanwhile, the gender pay gap in the APS - the difference between average male and female base salaries - fell to 7.8 per cent, the smallest ever reported. The commission said this was due to the "representation of male and female employees at the highest classification levels ... moving towards parity".
Across all industries in Australia, wages rose by 2.3 per cent last year.