While half of federal government employees plan to stay put for at least the next three years, an annual census of APS workers shows 24.5 per cent want to get out in the next 12 months and a further 25 per cent plan to leave within a year or two.

The figures highlight concerns that the public service is struggling to retain skilled and experienced staff, exacerbating capability gaps in the public service workforce.

The Australian Public Service Commission has warned that there is a vigorous contest for talent in the labour market and worker expectations of employers is evolving.

"To address critical capability gaps in this environment, the APS needs to understand what attracts people to the service, position itself as an employer of choice, and adopt strategic and targeted recruitment at all levels," the Commission said.

APS employment data shows there was a 4.9 per cent fall in recruitment last financial year while the number leaving the APS jumped to almost 10,300 (excluding 1809 Australian Signals Directorate staff who left coverage of the PS Act), a rise from the previous year.

Public service hiring consultant Kathy Kostyrko, a director of recruiting firm Hays, said the fact that so many staff were thinking of leaving their jobs should put managers on alert.

"It's a heads up," Ms Kostyrko said. "I wouldn't panic [but] the unemployment rate [in Canberra] is so low, people are seeing that there are opportunities elsewhere."

Of those who flagged their desire to quit, 24.5 per cent complained of a lack of career opportunities, 12.5 per cent wanted to change their career or type of work, 8.2 per cent were dissatisfied with senior leadership, 7.6 per cent reported the working environment was "unpleasant" and 6.1 per cent found the work unsatisfying.

Strikingly, given widespread wage stagnation and cost of living pressures, just 4.9 per cent wanted to leave their agency in search of a bigger pay packet.

The survey was undertaken before Prime Minister Scott Morrison announced a major restructure of the public service last week.

Professor of Human Resource Management at the University of Sydney Business School, John Shields, said the results are in line with research that "shows clearly that negative culture, lack of job challenge and lack of opportunity for career growth are some of the main reasons for exit. Pay is generally a secondary factor".

Ms Kostyrko said heavy workloads and limited promotion opportunities may be fueling dissatisfaction.

"Sitting in the same role year after year can be frustrating and career limiting," she said.

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Community and Public Sector Union National Secretary Melissa Donnelly said the census results showed the detrimental effect government job cuts were having on the public service.

Ms Donnelly said 18,908 public service jobs had been cut since 2013, "causing enormous damage to the capacity of the Commonwealth to deliver policy and essential services that all Australians rely upon".

She said the cuts, combined with the average staffing level (ASL) cap introduced in 2014-15, were placing increased pressure on public servants.

In a workplace health and safety survey of three government departments, Defence, Prime Minister and Cabinet and Human Services undertaken by the CPSU last financial year, more than a third reported that high job demands, poor support and change management and low job control was taking a toll, Ms Donnelly said.

"As long as the government continues to cut staff and enforce the ASL cap, results like these will continue," the union leader said.

Australian Public Service Commissioner Peter Woolcott said a program to improve career opportunities and work conditions for professionals working in the public service could go some way toward increasing retention of skilled and highly qualified APS staff.

The initiative includes identifying career pathways, fostering professional networks and providing learning opportunities. Initially the program is focused on human resource professionals, but will be expanded to include digital and procurement specialists.