Workers in the department were told on Friday that jobs in the vital Border Compliance Division would be first to go, but Agriculture bosses insist they can protect the nation's biosecurity despite the cuts.

The axe will fall first at the division's passenger, mail and cargo units, monitoring programs in regional Australia, as well as head office in Canberra.

The federal opposition said on Sunday the move would strike at the heart of Australia's image as a ''clean, green'' food-producing nation.

Departmental secretary Paul Grimes told 5200 workers on Friday that attempts to reduce staff numbers at Agriculture through ''natural attrition'' had failed, and the department wanted up to 220 of its workers to take redundancy payouts.

The Department of Agriculture, Fisheries and Forestry was $48.2 million in the red at the end of the 2012-13 financial year and new boss Mr Grimes warned staff to expect another deficit, the third in a row, this financial year.

Agriculture is the latest in a string of agencies and departments to try voluntary redundancies in an effort to reduce their workforces because the Abbott government's natural-attrition strategy has failed to deliver reductions since September's election. ''Natural attrition alone has not been sufficient to achieve the necessary staff reductions,'' Mr Grimes told staff.

''We will need to continue reducing staff across the department.

''We anticipate that in the order of 220 VRs [voluntary redundancies] will be required in coming months.

''In the first instance, offers will be made in Border Compliance Division in Canberra and the passengers, mail and cargo programs in the regions,'' he said.

The Border Compliance Division works with other federal agencies, and state and territory authorities, and industry to manage Australia's bio-security system to combat the threat posed by exotic pests and disease.

But Mr Grimes insisted the department would be able to safeguard the nation's bio-security.

''The analysis we've done and continue to do, including through the transition committees, will allow us to manage bio-security risk effectively,'' he said.

But opposition agriculture spokesman Joel Fitzgibbon said the job losses within the department would strike at Australia's frontline defences against introduced plants and diseases.

''They're basically cutting frontline services,'' he said.

''This is the worst possible place to be cutting.

''Our clean, green, safe image as a provider of food to the world is of critical importance and these cuts, of course, will put that reputation at risk.''

Mr Fitzgibbon said the Border Compliance Division was vital to protect the security of Australia's food supply as well as its exports.

''This is a threat to our own food that we consume ourselves and it's an enormous threat to our export income,'' he said.

''We export two-thirds of what we grow in this country and if we are to maximise the benefits presented by what I call the dining boom in Asia, we need to maintain that safe, clean and green image.

''It's critical to our success.''