The Australian Public Service Remuneration Report 2021 has also shown more women in senior roles has reduced the APS's gender pay gap, but men still earn 6 per cent more than their female colleagues.

But senior executives received a 4.2 per cent increase to their base salary in 2021, compared with a 3 per cent bump for non-executives.

SES 2 staff received the largest boost - 4.3 per cent - while those at the APS 2 level received the lowest increase of just 1.6 per cent.

The report said a number of factors played into higher wage rises for executives, including a lift on a suspension to remuneration increases in June 2021, and some executives having their vehicle allowance folded into their base salary.

Executives' ability to negotiate individually with their agency also accounted for the disproportionate rise, the report suggested.

"Given the small size of the SES cohort, population changes can easily impact median values," it said.

"Almost one quarter of SES employees covered in this report were promoted, engaged or transferred at level during 2021, giving one in four SES employees the opportunity to negotiate a new individual arrangement."

Annual wage increases for public servants have steadily shrunk since 2017, reaching a nadir when COVID-19 struck in 2020.

SES wages were slashed by 0.1 per cent that year, while non-executives received an increase of less than 1 per cent.

Non-senior executive employees received a median pay increase of 3 per cent in 2021, partly driven by a six-month deferral of non-SES wage increases in 2020.

"[That] had a substantial influence on non-SES base salary movement," the report said.

"[It] resulted in the majority of non-SES employees receiving two wage increases in 2021: the deferred 2020 increase and the scheduled 2021 increase."

The average base salary for male public servants was $102,112 - up from $99,082 in 2020 - compared with $96,006 for their female colleagues - up from $92,536.

The report found the gender pay gap, which dropped to 6 per cent from 6.6 per cent a year earlier, was "primarily" the result of men being overrepresented in senior roles.

But it said female representation in higher-ranking positions was edging closer to gender parity, a major influence in the shrinking gender pay gap.

"The data shows that women have historically been underrepresented at higher classification levels (EL 2 and above) and overrepresented at lower classification levels (APS 2-6)," it said.

"From 2020 to 2021, the representation of male and female employees at most senior classification levels moved further towards parity. In 2021, females represented over 50 per cent of EL 2 and SES 1 employees."

Women now accounted for 44.1 per cent of SES 3, the highest-ranking executive level, up from 40.9 per cent.

Larger increases have occurred in the two lower senior executive categories, SES 2 (46.4 per cent, up from 38.7 per cent) and SES1 (53.4 per cent, up from 45.5 per cent).

Women made up a smaller percentage in a number of lower-ranked roles, including APS levels 1-4.

The report found changes to reporting had "dramatically reduced" the number of bonuses issued to non-executive staff, with just 0.8 per cent of staff - or 1100 in total - receiving one.

At the executive level, that figure remained steady at 4 per cent.