The states of New South Wales and Queensland are dotted with restricted areas in their efforts to control the outbreak.
Thousands of horses and their owners are affected by state-wide lockdowns that seem unlikely to be lifted any time soon.
It was never going to be easy. No one needs reminding just how contagious this disease is. And therein lies the central issue.
Initial reports painted a picture of a disease spreading like wildfire through an equine population never before exposed to the virus.
Investigations linked the spread to a one-day event at Maitland in New South Wales.
It appeared the disease, believed to have arrived in Australia through an infected Japanese stallion, had somehow been conveyed to that event, and then dispersed further afield as competitors took their horses home, even as far as Queensland.
A formal inquiry into the spread will be conducted by a retired High Court judge, but the issue of immediate importance is containment.
The spread of the disease has slowed to a trickle thanks to containment strategies. But a trickle is not a halt. Authorities say they are still linking new cases back to the initial spread, and are looking at ways of stopping the virus from spreading within restricted areas, some of which have very dense horse populations.
Containment has clearly been effective in slowing its spread, but to ultimately stop its spread, the trickle needs to become a halt - no new cases outside restricted zones.
Up to 20 per cent of horses with the virus show no clinical signs, making containment doubly difficult.
There are some who feel, even now, that vaccination is the only option, going forward.
Australia and New Zealand have been the only nations with major equine populations to remain free of the disease.
Vaccination is a reality in most countries.
Is it such a big deal?
The vaccine is not cheap and there is more than one strain, and reports suggest there is no one vaccine to cover all strains. A second shot is required a month after the first. Horses can suffer a mild fever as a result of the vaccine. They need rest after the injection.
It will be a significant cost for many horse owners.
Vaccination supporters would argue, with some validity, so what? The industry is shouldering a hefty cost in the wake of the current outbreak.
While there are more serious horse diseases, the impact of the virus should not be underestimated in a population with no natural resistance.
While some cases are mild, others are severe, with full recovery times stretching many weeks. Complications such as heart problems and secondary infections are more common with equine flu than other respiratory infections.
It can kill older animals and the mortality rate among foals is of serious concern - up to 40 per cent has been recorded in outbreaks in other countries. It can cause mares to abort.
NSW's chief veterinary officer Bruce Christie is clear that the seriousness of equine flu should not be underestimated. "To suggest we are trying to eradicate a disease that would have a minimal effect on our horses is far from the truth," he said.
"On top of losses through mortalities, owners could face large veterinary bills, and also loss in productivity where horses are used in businesses."
But there are other considerations, too.
If Australia manages to contain the virus, what are the chances of another outbreak?
The modern era of transporting horses by air means horses can be relocated just about anywhere in the world in little more than a day. Containment of any disease will only be as effective as the quarantine services at both ends of the journey.
Then there is the insistence of the thoroughbred industry on natural cover of mares. Shuttle stallions travel the world doing their duty.
Artificial insemination has been the norm in many animal-based industries for many years, including standardbreds. DNA testing no longer leaves any room for doubts over the parentage of any horse.
Is it time the industry looked towards this option?
Dr Phil McManus, from the University of Sydney's School of Geosciences says equine flu was an almost inevitable consequence of the thoroughbred industry's insistence on natural insemination.
The world-wide travel of thoroughbreds and a suspected breach in quarantine procedures has combined with ineffective back-up measures, he argues.
"There has been a lack of understanding once this virus did get out. We have had people moving around spreading the disease accidentally.
"At this stage it still can be stopped. But there will be considerable fall-out from all of this."
The fall-out will include calls to change breeding regulations and allow AI. "And there will be a reduced foal crop for next year," he adds.
Darley Stud's Australian general manager, Oliver Tait, in confirming the disease at its premises at Aberdeen, in NSW's Hunter Valley, said: "EI is spreading quickly and we were not surprised when a small number of our yearlings began to display clinical signs of the virus."
Darley at Aberdeen has been restricting the movement of people and horses on and off the property since August 16, in addition to strictly adhering to bio-security protocols.
"It is apparent that the virus is airborne as our NSW property has been in lockdown for two weeks," Tait said. "We have continually been seeking advice from leading epidemiologists in the UK and USA since the outbreak of EI in Australia and their advice to us is that vaccination is unequivocally the only way forward.
"Containment efforts have probably assisted in slowing the spread of the virus but it is clear that they have not stopped it. Surely we now must focus on a vaccination strategy rather than a restriction of movement in order to stop the spread of EI into other parts of Australia."
He is not alone in that call. Well-known Australian veterinarian John Walker has been quoted in the media, describing the containment and eradication as fundamentally flawed.
He suggests Australia should vaccinate to get on equal footing with the rest of the world.
New zealand, too, must face important questions in the fall-out from the Australian experience.
A Canterbury equine veterinarian was quoted in a local newspaper as saying the chances of the virus eventually reaching NZ shores was "eight out of 10".
For now, the focus is on containment, and it seems it will not be long before Australia will learn whether the disease, which can be transmitted on clothing and equipment and can spread by air for up to 50m, will ultimately be beaten this way.
Failure will mean little choice but to sign up for the importation of industrial quantities of vaccine and place Australian on that "equal footing".
Success, on the other hand, will mean eventual elimination of the the disease from Australia's shores, but for how long?
Hard questions will remain.