On Wednesday, the latest Australian Public Service Remuneration Report showed the extent of the government gender pay gap for the first time, finding across the entire workforce the average base salary for women was $84,104, well below the $92,036 base salary for men.

Public Service Commissioner John Lloyd said the pay gap was well below the private sector where women are paid 19.6 per cent below men.

Community and Public Sector Union national secretary Nadine Flood said it was time for the Coalition to take action and for the former Labor government's pay equity provisions to be reinstated in enterprise bargaining agreements.

Calling for promotion of women to senior APS roles and more flexible working arrangements, Ms Flood said the report showed ongoing pain caused by protracted enterprise bargaining disputes, with the median base salary movement for non-Senior Executive Service workers rising by just 0.3 per cent last year.

"Governments should be using bargaining to bridge the gender pay gap, rather than freezing wages unless workers accept cuts to existing rights as the Turnbull government has done."

"It's 2017," she said. "There's no excuse why women and men shouldn't be getting paid the same for work of the same level, whether they're working in a Commonwealth department or the private sector."

"It's an indictment of the Turnbull government that their Public Service Commissioner John Lloyd says that an 8.6 per cent gender pay gap in the Commonwealth public sector isn't that bad because the private sector does even worse.

"He misses the point that that is an industry-to-industry comparison, while here we're talking about a gap within one employer."

Ms Flood said Mr Lloyd hadn't justified "his harsh and unreasonable approach to enterprise bargaining".

"A median pay rise of 0.3 per cent, which reflects the fact that tens of thousands of workers haven't had a pay rise for more than three years, is a disgrace," she said.

"We also know from our gender equality survey and from the government's own data that more needs to be done to get more women into senior roles.

"Flexible working arrangements for people with kids and elderly parents to care for is an important part of changing that gender mix at the top. Instead we've had John Lloyd attacking family-friendly working conditions at all levels of the public sector."

Labor senator Jenny McAllister said women's under-representation in senior APS roles remained a problem and there was evidence that traditional female-dominated departments had poorer pay than some central agencies remained.

The report showed women earn slightly more than men, on average, in five employment categories - the highest being at the APS 6 level where women make 101.6 per cent of mens' median income, or $88,194 compared with $86,844.

On Friday, Mr Lloyd called the union's comments inaccurate.

"In the APS there is no significant difference in pay between genders at individual classifications," he said in a statement.

"It is a strength of the APS that employees are paid the same for work of the same value.

"The statement by the CPSU that 'there's no excuse why women and men shouldn't be getting paid the same for work of the same level, whether they're working in a Commonwealth department or the private sector' erroneously suggests that such differences occur in the Australian Public Service.

"The 2016 Remuneration Report shows there is no gender pay gap on a classification basis."

Mr Lloyd said the government's bargaining policy was not gender biased.

"The reason for a low annual remuneration increase for some staff is that the CPSU has opposed pay offers. The CPSU's own action has denied its members and others a pay increase for up to 3 years," he said.

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