Nearly 500 jobs will be lost at the Federal Department of the Environment over the next three years.

Public servants based in Canberra were told at a meeting today that 480 staff will lose their jobs over the next 36 months.

They were told 250 of those positions will go by the end of this year.

The Community and Public Sector Union (CPSU), which represents public servants, says the job cuts will affect the department's ability to protect the natural environment.

CPSU national secretary Nadine Flood says the community expects the government to protect iconic environmental assets such as Kakadu, Antarctica and the Great Barrier Reef.

"You need talented experienced people to do that and cutting 480 jobs means fewer people on the ground who are doing that work," she said.

"These latest cuts bring the total tally of job losses announced by the Abbott Government to well over 5,500 nationally."

Positions at executive levels 1 and 2 will be the primary target of the predicted job cuts, with a 26 per cent reduction in senior executive service (SES) numbers anticipated.

The latest round of cuts comes on top of almost 200 positions which are being shed in the current round of voluntary redundancies.

Department faces cuts of $100 million over four years

Staff were told the latest cuts are to help the department remain within its budget.

A strategic review says structural change will reduce the department's operating budget by $100 million over four years, from $460 million in 2013-14 to $361 million in 2017-18.

Public servants were also told that if the requirements for job losses are not met through the voluntary redundancy round, then a merit-based process would be introduced.

The union says this announcement is concerning for nervous staff waiting for next month's federal budget.

"These are real people with families, bills and mortgages to pay," Ms Flood said.

"It is very stressful for staff in the Department of the Environment and other places where jobs are being cut.

"We are of course working with the department to ensure that all redundancies are voluntary and we save as many jobs as we can."

Changes across the public service recommended by the Commission of Audit have not yet been introduced, so the department's final job loss figures could be larger.

A large number of staff from the now defunct Federal Department of Climate Change and Energy Efficiency were moved into the Department of the Environment prior to the change of government last year.