Public Service Commissioner John Lloyd also defended a modest increase in senior executives' salaries, saying many of the officers had lost other benefits.

The Australian Public Service's latest remuneration report shows most staff's salaries didn't budge last year as the long-running stalemate on wage deals dragged on.

At some job levels, median total pay, which includes superannuation and other benefits, actually fell.

Meanwhile, senior executives' pay climbed a little: the median salary of SES officers rose by 1.4 per cent in 2015, while their total remuneration increased 0.6 per cent.

Community and Public Sector Union chief Nadine Flood criticised the different outcomes for junior and senior staff, saying politicians were "giving themselves and their most senior executives decent pay rises at the same time as they try to starve out lower-paid workers who are just trying to provide for their families".

However, Mr Lloyd said most of the increase in senior executives' salaries was "due to the rolling of benefits into base salary".

"It is not, as the CPSU [says], from 'giving themselves decent pay rises'," he said.

"It is either disingenuous, or dishonest, of the CPSU to paint a picture of professional senior public servants giving themselves pay increases at the expense of their colleagues.

"The single biggest hurdle to non-SES Commonwealth public servants receiving 2 per annum wages increases is the CPSU itself.

"It is time the CPSU stopped getting in the way of its members putting in place new enterprise agreements that deliver wage increases."

Total pay across all industries in Australia rose by an average of 2.2 per cent last year.

Wage deals covering most public servants expired more than two years ago, in July 2014. About three in four APS staff still lack a new agreement.