Farmers have warned the impasse could spark food shortages and drive supermarket prices higher if produce is left to rot during upcoming harvests.

The draft agriculture code covers workers, farm businesses and agricultural services, along with seasonal temporary migrant workers.

It aims to ensure consistency in cross-border movement rules for agriculture workers while also ensuring coronavirus safety.

AAP understands the Australian Health Protection Principal Committee - made up of federal and state health officers - failed to unanimously endorse the code on Tuesday night.

Agriculture Minister David Littleproud said Australia's system of government was being tested in a crisis.

"These border issues are now a real test of our federation," he told AAP on Wednesday.

"This is an opportunity for states to show us that federation works for all Australians, not just those in capital cities."

While South Australia has relaxed border zones to 40km, many farm-related movements are still severely curtailed.

NSW and Victoria have agreed to 100km agriculture buffer zones, but that distance also continues to restrict some movements.

Queensland is the only state with an agriculture code to facilitate industry movements across borders.

It is understood Mr Littleproud is refusing to back down from the draft national code, which will be discussed at Friday's national cabinet meeting.

The document sets out principles including a pledge that agriculture movements will not be unnecessarily impeded by border rules.

Border workers would need to carry face masks, gloves and hand sanitiser, as well as keep records of movements and contacts.

National Farmers' Federation president Fiona Simson said with fruit, vegetable and grain harvests approaching, food could be left in paddocks to rot.

"This is not only a devastating kick in the gut for farmers and regional communities who have faced years of drought, but will impact the price and availability fresh food across Australia," she told AAP.

She said there were grave concerns national cabinet would fail to settle on a code.

The NFF president criticised a panicked approach in some states to border restrictions, calling for common sense on movement relating to food and fibre production.

"It's nonsensical that movements predominantly between from areas with zero active or recorded cases are prohibited," Ms Simson said.

"The stretch of land between Mildura in Victoria to Longreach in Queensland has zero active cases. Why are we restricting these movements based on artificial state boundaries?

"Farmers and regional towns are suffering. Enough with the city-centric, bureaucracy driven, out-of-touch approach."

Australian Associated Press