Health dept job cuts 'won't hit patients'

Patients and frontline health services will not be affected by the loss of 250 jobs at the federal health department, its boss insists.

The Community and Public Sector Union warns frontline services for patients could be affected as a result of the department shedding five per cent of its 5000-strong workforce.

The union says it's unlikely such a significant loss of staff would have no impact.

Department secretary Martin Bowles insists the responsibilities of the department will continue to be fulfilled.

"This notion of services being cut is quite frankly not true," he told AAP.

"We don't run the hospitals. We don't provide those sorts of services."

Mr Bowles said the cuts will come partly from natural attrition with the remainder from voluntary redundancies, to be completed before July.

"It's about getting our staffing to a level that is sustainable in the longer term to deliver what the government is asking us to deliver," he said.

The department insists retention of specialist skills will be a priority in any decisions to offer redundancies.

CPSU deputy secretary Beth Vincent-Pietsch believes 250 fewer people on the ground and a loss of corporate knowledge will certainly have an impact.

"I am worried that 250 jobs, five per cent of employees, is a fair whack," she told AAP.

"I'm yet to see how they can have such confidence that it won't affect frontline services.

"It's not like they've got a lot of fat to trim."

She said at least 40 of the job losses will come from the department's health provider compliance division, which is set to be restructured.

The department ensures the correct Medicare and pharmaceutical benefits are paid to the correct people, and the union is concerned some of the work will now be automated.

"It does very critical work and if it's not handled carefully, it could have a bad impact," she said.

The union will meet with the department on Friday.