A new report shows women in the public sector are paid on average 8.6 per cent less than men.

The latest Australian Public Service Remuneration Report says the average base salary across the workforce for women is $84,104, as opposed to a $92,036 base salary for men.

Public Service Commissioner John Lloyd has pointed out that the pay gap is well below the private sector average of 19.6 per cent, but Community and Public Sector Union national secretary Nadine Flood says it can be closed even further by bringing in pay equity provisions in enterprise bargaining agreements.

“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,” 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.

“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.”

Mr Lloyd said the union's take was not accurate, and denied a gender bias in the government’s bargaining policy.  

“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.

“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.”