Secretary for the prime minister's department Martin Parkinson issued a call-to-arms in an end-of-year speech that also urged the federal bureaucracy to better prepare new MPs, ministers and staffers for their jobs.

Dr Parkinson warned declining public faith in democracy had coincided with a reported crisis in confidence in the bureaucracy's ranks and anxiety among staff about the retreat of liberal democratic values.

He said public faith in government agencies relied on their competence in delivering services, and identified a change that would make the bureaucracy more capable.

Warning against governments making ill-justified rearrangements inside the federal bureaucracy, Dr Parkinson said frequent restructures turned the focus of agencies inwards.

"Our experience is one of frequent restructuring – for reasons that are unclear to the restructured and those looking on," he said.

"The result is disorienting for our partners and disruptive for our staff. And more so if there is no compelling rationale for the change – for example, if the change is driven by a political logic, such as rewarding a minister, rather than improving the lot of the citizen."

Dr Parkinson's address to public servants at an Institute of Public Administration Australia event in Canberra called for more stability and said needless machinery-of-government changes could be avoided by having agencies simply report to more than one minister.

"Institutions and organisations take time and effort to build but are quickly weakened and damaged – if they deserve condemnation and reform, that should occur, but if not, I would urge caution and counsel against regarding the APS as a set of Lego blocks to be painlessly re-created," he said.

The bureaucracy had also done too little to support MPs and their offices taking charge of portfolios with scant training, Dr Parkinson said.

"Our politicians and their staffers, whose actions and decisions have important consequences for Australia, receive no prior training before taking up positions that are central to our democratic process," he said.

"Think about that – no training on the operation of government, their personal roles and responsibilities, or the separation between the apolitical public service and their own, correctly, political roles."

New staffers and parliamentarians could find it hard knowing how to work properly and most effectively with the public service to pursue their agenda.

"I cannot conceive of any other serious company or organisation, where we require people to take on important roles without at least some form of prior training – anywhere else, it would seem quite bizarre," Dr Parkinson said.

"Yet this is the position in which ministers and their advisers continue to find themselves. This is an area where we could easily do better, and it might help improve the functioning of our democratic system."

Australia's top public servant said a leader of a major review into the federal bureaucracy, David Thodey, and former Prime Minister's department boss Peter Shergold, had reported a crisis of confidence in its workforce.

This had coincided with decline in public faith in democracies, occurring regardless of the political party in power.

"When our partners and the public doubt our capability and integrity, it is not surprising that we come to doubt ourselves," he said.

"They mistrust our beneficial intent – they doubt that we in fact intend to do the right thing. And they also mistrust our competence."

Disquiet about the public service's future, and anxiety over the retreat of liberal democratic traditions, plagued more than two-thirds of the public sector’s most motivated employees.

"This pessimism could not come at a worse possible time – when confidence in liberal democracy is at an all-time low and disillusioned voters are increasingly attracted to simplistic responses to complex public policy conundrums," Dr Parkinson said.

Remedies inside the Australian Public Service would be grounded in a "deep confidence" in liberal democratic values and institutions.

"Confidence in our values brings clarity of purpose," he said.

"The APS also has to contribute to the health of our democracy by guarding our independence and providing advice without fear or favour."

Public trust in the bureaucracy would also depend on its success in adopting technology, he said.

The review of the federal bureaucracy is expected to report by mid-2019.