Professor Michael Studdert, of the Veterinary Virology School of Veterinary Science at the University of Melbourne, says accepting the disease would still mean cancelled race meetings and other equestrian events, as well as lost performance days and the ongoing costs of treatment and vaccine.
It would also mean the imposition of restrictions on the movements of horses to other countries, including New Zealand.
"For those countries that accept equine influenza as an endemic disease, the annual costs of living with the disease are very high," he said.
Professor Studdert says equine flu is endemic in most countries, with the exceptions of South Africa, Japan, New Zealand, and Australia
"South Africa has had two equine influenza outbreaks in recent years and Japan, prior to the [recent] outbreak, had recorded a single outbreak in 1972. The success of South Africa and Japan in eradicating equine influenza is the path that Australia should pursue until the last case."
The professor, acknowledging the strategic use of vaccine for restricted at-risk populations, warned that its widespread use would only complicate and prolong efforts to control and eradicate equine flu.
Such widepsread use should be an "almost last-resort action", he said.
Professor Studdert, in a report he prepared on the outbreak, described it as one of the most significant animal disease emergencies in Australian history.
"If the current, highly coordinated efforts to identify all infected premises in Australia and restrict movements of all horses can be sustained, and there is continuing strong support and full cooperation from all involved with the industry ... we should be able to achieve eradication.
"The challenge for Australia is to eradicate equine influenza and restore the equine influenza-free status that existed before the present introduction."
Protocols for the importation of horses have been in place for decades, he says, and are regularly reviewed.
"Prior to the entry of the equine influenza virus into Australia ... these protocols have been generally successful.
"There was a single introduction of an exotic virus disease in 2001 when West Nile virus was carried by an infected shuttle stallion from Canada into the Eastern Creek quarantine station in western Sydney. The infected stallion became seriously ill and euthanasia was considered imminent.
"The horse recovered and was released from quarantine and there was no further transmission of the virus."
Such transmission would not have come from the infected stallion since horses are considered 'dead-end' hosts for the virus, which is spread by mosquitoes from birds.
"In contrast to West Nile virus, equine influenza is a self-limiting disease. Individual horses clear the virus within two weeks following infection and there is no long-term carrier status after recovery and there are no known alternative or reservoir hosts. These features render equine influenza eminently controllable and eradicable."
The professor said there remains uncertainty about the events that allowed the introduction of equine influenza virus into Australia, but "it seems that there may have been a series of departures from generally accepted quarantine protocols".
He said the first matter to be explained are the circumstances that allowed its introduction to Australia, apparently in horses from Japan.
"It is notable," he said, "that the first diagnosis of equine influenza in Japan was one week after the horses left Japan for Australia.
"There are important matters for enquiry here. Pre-embarkation protocols for horses travelling to Japan and to Australia should have guaranteed that no equine influenza virus could enter either country and, similarly, post-arrival quarantine protocols should have guaranteed that if the virus did enter it should not have escaped to the general horse populations in either country."
Events after arrival appear to have allowed the transmission of equine flus from one of 13 stallions from Japan to other horses in New South Wales and Queensland.
"It is likely that all the shuttle stallions that left Japan for Australia were vaccinated and that vaccinations were current.
"Vaccination presumably masked the overt clinical presence of equine influenza virus in those horses.
"It would be of interest to know more about the detail of the events in Japan and these events - like those in Australia - should be the subject of considerable further formal and independent enquiry."
Professor Studdert praised the response of authorities to the outbreak.
"The Australian response to the outbreak has been remarkable and effective. The internet sites set up by the Commonwealth and the States - particularly the NSW Department of Primary Industries site - provide an extraordinary example of disease control in a modern age.
"These sites, preserved, will provide a valuable record of the events and a wonderful teaching resource for the next generation of students and for all involved in the control of infectious diseases."