A report also reveals near-perfect pay equality between male and female public servants employed at similar levels, though men still dominate senior ranks.

Staff's median base pay increased by 5.9 per cent in 2012, while the salaries of senior executives rose by 4.7 per cent.

The median pay rise far outstripped national wages growth, which the Australian Bureau of Statistics says was 3.4 per cent over the same period.

The typical federal public servant in Canberra, an executive level 1 officer, was earning $104,825 a year as of December 31, plus an extra $18,508 in superannuation and other benefits.

Three years ago, the federal government moved to restrain average annual wage growth in the bureaucracy to 3 per cent a year.

Agencies were permitted to negotiate higher wage rises for staff, but the Finance Department vetoed many of those deals.

The Public Service Commission, which published the remuneration report, said the rapid pay growth in 2012 was ''not inconsistent'' with the government's wage restraint policy.

Rather, the pay rises were linked to a lack of new jobs and promotions, with the number of new positions falling by 24 per cent last year from 2011.

Fewer vacancies meant public servants had tended to stay in their jobs rather than seek a promotion, and therefore were more likely to move up the pay scale within their current classifications.

''The key influence in 2012 has been a reduction in vacancies being filled, leading to fewer promotions and lower workforce mobility,'' a commission spokeswoman said.

''A greater proportion of employees have remained in their current position and have moved up within the pay band for their classification, as well as receiving a general pay increase as contained in their agreement.''

The report also said agencies were employing fewer temporary staff, who tended to be hired at the lowest pay point.

Most government agencies have phased out performance bonuses, or are in the process of doing so. However, three in 10 senior executives were paid a bonus last year.

The median bonuses ranged from $8519 for SES band 1 officers to $19,997 for band 3s.

Community and Public Sector Union national secretary Nadine Flood said the report confirmed the union had won solid outcomes in the last round of pay bargaining.

''We are proud of the fact our bargaining efforts delivered a better than 3 per cent increase for more than three-quarters of APS staff,'' she said.

''These increases came through a combination of base pay rises and other classification changes.

''One of the union's main aims in the last round of bargaining was to improve pay equity across the APS and we made some important progress in that area, particularly for members working in agencies with the lowest pay rates.''

Women's median base pay was within 1 per cent of men's pay at all job levels, though it was marginally lower for APS1s and marginally higher for SES band 3s.

But while women make up 57.4 per cent of the federal bureaucracy's workforce, they comprise only 39.6 per cent of SES ranks.

The commission's latest remuneration report did not compare public servants' salaries with private sector pay.

However, past reports showed that public servants generally earned less than similarly skilled workers in the private sector, especially at senior levels.