The median base salary for staff below the senior executive service increased by just 0.1 per cent in 2014. In the previous nine years, the annual increase averaged 4.2 per cent.

SES officers fared almost as poorly: their median salary rose 0.2 per cent last year.

The Abbott government attributed the unprecedented outcome to unions, saying they had advised their members to reject pay offers worth "millions of dollars".

But the Community and Public Sector Union said staff were unwilling to give away crucial conditions and rights in return for historically low pay rises.

In contrast to the APS's stagnant salaries, wages across Australia increased by 2.6 per cent in 2014.

Wage deals covering about 150,000 public servants expired almost a year ago. Agencies have since struggled to develop new agreements that satisfy staff while adhering to the government's tough rules on pay restraint.

The typical federal public servant, an APS level 6 officer, had a median salary of $86,844 on December 31, 2014 and total remuneration (including superannuation, allowances and other payments) of $102,246.

While bargaining delays contributed to last year's negligible salary growth, the result also shows a larger proportion of public servants have now "maxed out" at their present job level and can no longer accrue performance-based pay rises.

Acting Employment Minister Christopher Pyne said the CPSU had prevented staff from accessing the "responsible wage rises currently on offer".

He said the staff in the bureaucracy's largest workplace, the Department of Human Services, had missed out on "millions of dollars in pay" because the union rejected a proposed 1.5 per cent-a-year increase that would have come into effect in August 2014.

"The CPI since then [has been] 0.8 per cent annualised and the employee living cost index 0.2 per cent annualised, so on any measure [the department's] employees would have been well ahead of inflation had the CPSU not blocked this offer being put to staff," Mr Pyne said.

Despite negligible pay growth last year, Mr Pyne said public servants had enjoyed wage rises considerably higher than those the general workforce received over the past decade.

He said that, with inflation low, the union's "absurd claim" for a 4 per cent a year pay increase was "totally out of touch with Australia's current economic circumstances".

"Unlike the union, Australian Public Service employees understand that the government needs to live within its means. To agree to the CPSU's claims would result in 10,000 job losses across the sector."

However, the union's national secretary, Nadine Flood, said public servants "would love a pay rise" but there were none on offer.

"What is on offer is cuts to conditions and rights, in return for pay offers averaging 1 per cent a year, which for many means an actual cut in take-home pay. Calling it a pay rise is disingenuous, if not dishonest," she said.

"On the rare occasions that agencies have been brave enough to put their low-ball offers to an all-staff vote, they have been resoundingly rejected," she said.

Ms Flood said public sector staff were now a year into an effective pay freeze and "staring at the prospect of nasty cuts to conditions and workplace rights".

She said the government's bargaining policy had been "an abject failure". "The government needs to rethink its approach or face more industrial action. It's their call."

Last month, the Remuneration Tribunal extended its freeze on the pay of federal politicians, judges and top public servants, saying it would defer its decision on their salaries until later this year.