There should be "no false expectations" about the ability to control feral animal populations should they become involved in an exotic disease outbreak, the government's own response plan says.
Feral water buffalo and pigs populations are named as the two biggest concerns.
However, the government has attempted to downplay concerns, highlighting international examples where feral animals played little to no role in outbreaks.
The AusVet Plan, which outlines the nation's response to a variety of animal and plant diseases, says few elements in an emergency animal disease (EAD) outbreak would "be less predictable or tractable".
"Wild animals can often pass through fences designed for livestock, and their movements could frustrate attempts to contain or eliminate an EAD," the document says.
"Infected wild animals might evade attempts to contain and eliminate them, and they can disperse a considerable distance."
The AusVet Plan outlines the risk potential for dozens of diseases to spread in feral populations, including foot and mouth, lumpy skin and African swine fever. The plan notes there was a small but possible risk of transmission between wild and domesticated animals
Although feral buffalo are restricted to the country's north, their distribution overlaps that of domestic cattle and in the wet season can gather in groups of up to 500 for breeding, which can increase the probability of disease transmission.
"Buffalo could be a source of infection for domestic animals.... there is now clear evidence from Africa of transmission from carrier buffalo and cattle under field conditions," the document states.
Their wallowing habits also increase the transmission of disease to other species and under stress herds may leave their home range and move into another herd's area.
Pigs are an amplifying host of FMD, because of their susceptibility to the disease and their capacity to excrete large amounts of the virus. Feral pigs are found in a wide range of habitats, including agricultural areas, where they mix with other feral and domestic animals.
Roaming, wallowing, high birth rate, and scavenging on refuse and carcasses all make feral pigs a dangerous vector of diseases.
In Europe, feral pigs have become infected with African swine fever and "could be a reservoir of the disease".
Deer and goats are potential disease spreaders, gathering in groups of up to 100 and 1000 respectively, and often intermingling with livestock.
"There should be no false expectations about the ability to control wild animal populations should they become involved in an EAD outbreak," the AusVet document states.
"In the longer term, the existence of wild animal carriers or reservoirs of disease will make it more difficult to demonstrate disease eradication."
The AusVet document outlines a comprehensive and complex response plan for feral animal disease outbreaks, which may include locally eliminating entire populations.
The document notes there were many factors that reduced the influence feral animals would have on a wide-spread outbreak, however, it also acknowledges it was a situation with many unknowns.
Agriculture Minister Murray Watt said based on advice from the department's biosecurity experts, international evidence suggested feral animals posed a low risk of transmitting diseases in an outbreak.
"It is not a zero risk, nothing is zero risk, but it's a real low risk of occurring," Senator Murray said.
"Based on the advice, I have confidence we are taking the appropriate steps to manage the risk."
Bulgaria is commonly cited as an example of where FMD got into the feral pig population with limited affect on the overall outbreak. However, Bulgaria has a feral pig population of under 100,000, compared to Australia's 26 million.
"I've said all along, I'll continue to discuss this matter with the department," Mr Watt said.
"If there is more we can do, we will do it. I'm certainly happy to consider what further action may need to be taken around feral animals."
The Centre for Invasive Species Solutions (CISS), a government-backed RnD organisation, has been leading the charge against feral animals, creating tools and weapons to fight them.
However, its federal funding runs out in less than 12 months. CISS has already been forced to wind down a number of projects, including its effective rabbit biocontrol program. Farming leaders have called on the government to guarantee funding to avoid the "cascading impacts" of CISS' closure.