Median base salaries in the Australian Public Service rose just 2.5 per cent in 2011. The typical public servant in Canberra – an executive-level 1 officer – now earns about $99,400 a year.

It was the slowest pay growth recorded since the Public Service Commission began reporting on remuneration in 2002. In contrast, the Australian Bureau of Statistics says private-sector wages rose 3.8 per cent last year.

However, Community and Public Sector Union national secretary Nadine Flood said the data was skewed because several large government workplaces struck new wage deals with staff early this year.

She said the report excluded pay rises awarded to about 27,000 APS staff in 2012, including those in the departments of Defence, Housing, Community Services and Indigenous Affairs, and Education, Employment and Workplace Affairs.

"Our research shows over three-quarters of APS employees secured pay deals that will deliver 3.5 per cent a year over the life of the agreement. However, it's also true to say that pay outcomes reflect the fact that this was the toughest round of APS bargaining in some years."

The median base pay of a senior executive in the federal bureaucracy increased 4.1 per cent during 2011. However, this was mostly due to a number of agencies phasing out performance bonuses and incorporating the money into salaries instead.

Last year, almost all federal departments and agencies negotiated new wage deals with their staff. The government imposed a cap on these agreements to save money, saying APS pay increases could not exceed an average of 3 per cent a year.

The commission's latest report, which details staff pay as of December 31, 2011, says graduates' salaries rose at a faster rate than that of every other level of public servant, increasing by 4 per cent over the year.

Graduates' median base pay was $55,162 a year, while their total salary package (which includes superannuation and other benefits) was worth $63,742.

The median base pay of executive-level 1 staff, who make up the largest cohort of federal public servants in the ACT, rose just 2.2 per cent to $99,378. Their median salary package was worth $115,630.

The report also notes that about four in five senior executives receive some form of car allowance, usually worth about $26,000 a year. However, fewer than one in 40 EL2 officers, and just one in 500 EL1s received the benefit.

Previous years' remuneration studies, which were carried out by consulting firm Mercer, found federal public servants typically received much less pay than similarly qualified staff in the private sector.

The 2010 report found an EL1 officer could earn an extra $8500 in base pay if they performed the same type of work for a company, or an extra $24,300 in total benefits.

The pay gap widened at higher levels, especially for top-ranked senior executives.