The Defence secretary and Chief of the Defence Force are considering next steps after some officials in the department signed a petition calling on the Albanese government to immediately cease all military exports to Israel.
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The open letter to Prime Minister Anthony Albanese is titled "Public servants condemn Australian Government complicity in Palestinian genocide", and demanded an end to "weapons support to Israel".
The federal government denies supplying weapons to Israel in the last five years, but it does export dual-use items, which are generally used for commercial purposes, but can have military applications too.
Defence is working through a list of more than 2200 public servants - across local, state and federal government - to determine how many of their staff have signed on.
Liberal senator Simon Birmingham asked the Defence bosses whether officials in the department who had signed the petition had breached their obligations, citing what he called, "erroneous or egregious statements" in the letter.
Defence secretary Greg Moriarty and Chief of the Defence Force Angus Campbell said they had not reached a conclusion on that point.
"APS employees have a right to express their views on issues of social, cultural or political significance in the community, but that right must be balanced by the obligations of APS employment," Mr Moriarty said.
"And the need to maintain confidence from the government and the broader community in the impartiality and the professionalism of the Australian Public Service."
General Campbell added that "there is an expectation and a requirement, that members of the ADF conduct themselves in a non-partisan and apolitical manner in the execution of their duties".
Mr Moriarty said the department "will look very seriously [at this]".
"[General Campbell] and I have already had a discussion about the need to reiterate our long-standing policy in relation to these matters and to look at the particular circumstances."
If steps are taken, it could range from reminding employees about responsibilities, to formal action in accordance with the APS Code of Conduct.
An official also said the Public Service Commission had sent agencies advice last Friday on "the APS policies, including social media policies and indicating that it was up to agencies to then look at the circumstances within their department".