The federal Health Department is seeking up to 250 voluntary redundancies.

Health department secretary Martin Bowles has emailed staff to explain that the agency wants “a staffing profile that is affordable”.

CPSU deputy secretary Beth Vincent-Pietsch said the cuts were equivalent to five per cent of the total Health Department workforce.

“We have serious concerns about the potential impact of losing that capacity and experience on the agency's essential work,” she told Fairfax reporters.

“We have begun talks with the department and will continue to closely monitor what impact this reduction in staffing will have on the services provided by Health, and ensuring affected workers are properly supported.

“It is at least encouraging that the department appears committed to a transparent process of voluntary redundancies.

“This reduction in staffing in the Health Department add to the 18,000 jobs cut across Commonwealth agencies in recent years and underpins just how wrong the Turnbull government's priorities are.

“Australians can't afford for the critical public role played by Health to be at risk or service standards to erode as they have in other agencies like Centrelink, Medicare and Child Support, the Tax Office.”

Mr Bowles had earlier warned that budget and staffing issues are the department's biggest challenges.