Victoria's chief veterinary officer Graeme Cooke has told a recent conference that there remained an "unprecedented" risk of an emergency animal disease arriving in Australia.
He said the threat was elevated during last year's foot-and-mouth outbreak in Indonesia and there remained at a 50 per cent chance of such a disease entering the country.
That was even with the recent "beefing up" of biosecurity at Australia's borders, he said.
Dr Cooke told the annual Victorian Farmers Federation conference that the Centre of Excellence for Biosecurity Risk Analysis, at the University of Melbourne, had estimated the most significant risk came from four diseases.
He said CEBRA estimated there was a 12 pc possibility of FMD entering Australia within five years, a 28pc chance for Lumpy Skin Disease, 13pc of African horse sickness and 21pc for African swine fever.
'They are trade-stopping diseases - the moment the commonwealth informs the rest of the world, then nations we trade with would say, 'thank you very much, but no more until things become a bit more clear'."
Victoria was a "special case," Dr Cooke said.
"This is a powerhouse of the agricultural economy, with 3 per cent of the land mass,' he said.
"We have all this agricultural activity happening, a lot of movement of trucks and people and a higher density and variety of different livestock, which some of these diseases like."
Victoria produced 20pc of Australia's lamb but accounted for 50pc of all exports; when it came to dairy, that figure was 60pc of exports.
Discovery of FMD would lead to an immediate livestock standstill, as the UK experience in 2001 and 2007 showed the disease moved through saleyards before being detected.
"Standstill is a way of stopping susceptible animals moving, by locking them down until tracing can be done," he said.
"It's a clear demonstration to the rest of the world Australia means business and is not going to let this proceed any further.
"The national livestock standstill is probably the greatest single thing we can do in the first 72 hours."
Part of the response would also be the introduction of livestock movement permits, he said.
Asked if the farming sector was ready to adopt a system of movement permits Dr Cooke said: "The system is ready but people have not got the habit of using it.
"In many countries in the world, you can't move an animal unless you have a permit," he said.
"That has never been easier, you can do it (get a permit) over the phone if you want to.
"There are various things that will support us enormously, like eID's in sheep - we have enablers there," he said.
But he said national veterinary authorities had not yet decided on how to roll out the permit system.
"Do we roll out the permit system on the day and then everyone has to try and learn to use it?" Dr Cooke said.
"It would be nice to find some way where it was bubbling through the system and people knew about it - then it doesn't have to be a seismic change.
"There are parts of the industry that it could suit, in terms of a quick register of a movement."
Any lockdown would also need to be "rational and proportionate.'
"A lockdown has to be rational, it has to be welfare base - the whole purpose of a permitting system is to ensure business carries on, where needed," he said.
"It's not actually locking every single animal down to its paddock, there has to be a reasoned approach
"Unfortunately, that comes with a bit of a risk, but you have to take those risks.
"There is always a 'coming to learn' what is proportional and what is not proportional and that is actually very much in discussions, between the states."
The federal government had ramped up its biosecurity protocols following the Indonesian outbreak, .
"They have really beefed up biosecurity at the border, with detection dogs, passenger profiling, greater levels of bag checking behind the scenes and increased fines," he said.
'The idea is to lock disease out - but we can't rely on that - that 50pc figure is with all this in place, not before it was done."
In Victoria, the state had committed $43 million in a "whole of government" approach to any disease incursion.
That included spending on improved IT and data handling, electronic permits and other capabilities.
"The clear desire is to get rid of a disease, as quickly as possible," he said.