As big enterprise agreement votes loom in the Defence and Immigration Departments, unions have seized on comments from Commissioner John Lloyd that public servants will not be able to legally enforce conditions which have been shifted into "policy".

The question has been at the heart of the disputes that have been raging across the 152,000-strong Australian Public Service since 2013, with Mr Lloyd and Coalition ministers insisting that large parts of enterprise agreements were being moved into policy in an effort to cut back on useless workplace red tape.

But unions have repeatedly told their members that the move was about stripping them of their workplace rights because policies could be changed without consulting the workforce and even if left in place, did not carry the same legal weight as provisions in a enterprise agreement.

Mr Lloyd was asked about the breastfeeding policies in the departments at Senate Estimates earlier this month and responded:

"œYou might say that it is not strictly enforceable, like the Fair Work Ombudsman might not be able to get involved and ensure that it is adhered to," the commissioner told the Senate committee.

"But the departments and agencies that have taken it out will replicate it in their policies and guidelines and they will respect the rights of breastfeeding mothers to be able to breastfeed in the workplace, as is appropriate, and in accordance with government policies."

Deputy Commissioner Stephanie Foster followed up by expanding on her boss' statement.

"Putting something in an agreement obviously has a status that a policy does not have," Ms Foster said.

"But the practical application is one that I think, in a real context—one that is actually happening in the workplace—is that agencies are supporting women returning from leave and they are making facilities available."

The Community and Public Sector Union says the exchange is a significant concession from the commissioner and union members at the anti-money laundering agency AUSTRAC, where about 260 public servants are preparing to vote on a proposed EA, that crucial rights are to be lost.

"With one third of your enterprise agreement gone under AUSTRAC's proposal, the fiction that removing rights out of enforceable agreements and into unenforceable policy will not affect you has been put to bed by the people overseeing their removal," the union bulletin states.

The Public Service Commission responded to questions from The Canberra Times with a statement.

"In designing an agency's framework for employment terms and conditions a number of factors influence the choice between enunciating them as policies or as a provision of an enterprise agreement," the statement read.

"The employer and employees will have regard to considerations like workplace and employee flexibility, management commitment, adaptability to changing conditions, employee coverage, interaction with other personnel management entitlements etc.

"Also, the interaction between an enterprise agreement and an agency's policy will depend on the statements contained in the various documents.

"Employees have various avenues for recourse against any unfair treatment that may arise from the application of agreement provisions or agency policies."