Federal public servants' salaries are stagnating, though their wages still rose slightly faster than other Australian workers' last year.

Median base pay in the federal bureaucracy grew by 3 per cent in 2013, the second-smallest increase in a decade.

However, most public servants face bleaker prospects this year: enterprise agreements expire next month, wage negotiations are well behind schedule and the Abbott government has all but ruled out back pay.

The typical federal bureaucrat in Canberra, an executive level 1 employee, had an annual salary of $108,013 in December, plus $19,055 in superannuation, vehicle allowances and other benefits.

The median salary of APS6 officers, the second-largest cohort of staff in the ACT, was $86,844, plus $15,005 in benefits.

Across government, junior staff fared marginally worse than their managers: median salaries within the senior executive service rose 3.8 per cent compared with 2.9 per cent for non-SES officers.

Yet the Bureau of Statistics suggests most public servants received higher raises than other workers: the national private sector wage index rose just 2.5 per cent over the same period.

The sharpest increase was reserved for graduates: their median base pay rose 6.9 per cent to $60,871, though the Public Service Commission attributed this shift to a single, large, relatively low-paying agency, which employed fewer graduate staff last year.

The commission also noted that graduates, from one year to the next, "are not the same employees - that is, individual graduates did not receive a 6.9 per cent increase in salary".

The other significant increase was awarded to band 3 senior executives - deputy secretaries - whose median salaries rose by 6 per cent to $300,000. Lower-level senior executives - bands 1 and 2 - had base pay rises of 3.7 and 3.9 per cent respectively.

The commission said a lack of new jobs and promotion opportunities meant public servants were staying in their existing jobs longer, and were more likely "to have reached the top of the salary scale for their classification".

The latest remuneration data highlights the vast gaps in pay between some public servants who are employed at nominally the same level.

APS6 staff, for example, had base salaries as low $61,989 and as high as $119,266 in December, while EL1 officers earned as little as $70,594 and as much as $275,669.

Earlier this year, Public Service Minister Eric Abetz ruled out trying to centralise government wage deals or even out pay differences, saying "the one-size-fits-all approach does not necessarily suit the huge variety of agencies that we have".