Farms are being released from forced quarantine after being caught up in the Japanese encephalitis outbreak earlier in the year.
A total of 23 Victorian properties have been released from quarantine where JEV "had been detected or suspected".
Up to five people are believed to have died, and about 70 piggeries in Victoria, NSW, Queensland and South Australia were isolated after the surprise outbreak from earlier in the year.
Many other people have been hospitalised with JEV.
There are 39 human cases in Australia - NSW 13, Queensland 2, South Australia 5, Victoria 9.
The official response to the JEV outbreak centred on piggeries which "amplify" the virus.
In May the NSW chief veterinary officer said testing of horse samples had identified 26 horses with probable JEV and a further four horses as possible cases.
Most biosecurity officials say the arrival of the cold, winter weather had helped slow the movement of mosquitoes which have spread the virus.
Until February this year, the disease was previously unknown in Australia.
"It is not known how the virus came onto mainland Australia, and it's the first time the virus has been detected in southern Australia. It is likely that the movement of infected mosquitoes or migratory waterbirds may have played a part in the virus' spread," the federal government says.
Most human infections of JEV cause no symptoms or mild symptoms such as headache or fever.
A person with severe disease may present with inflammation of the brain (encephalitis), characterised by sudden onset of vomiting, high fever and chills, severe headache, sensitivity to light, neck stiffness and nausea/vomiting.
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Children aged under five years of age and older people who are infected with JEV are at a higher risk of developing more severe illness.
There is no risk to humans from consuming pork or pig products. Pork products are safe to eat.
Agriculture Victoria lifted movement restrictions on all Victorian properties where Japanese encephalitis had been detected or suspected earlier in the month.
Authorities said effective measures to control JEV will continue including, vaccination of workers and families on pig farms and mosquito control, as required.
"Agriculture Victoria will continue to work with Department of Health on surveillance and disease modelling to improve our understanding of Japanese encephalitis in Victoria.
"While the risk of Japanese encephalitis has abated with the cooler weather, pig owners are asked to remain vigilant for signs of mosquito activity and Japanese encephalitis."
Now JEV is part of Australia's virus landscape, the return of warmer weather in spring is also expected to bring a fresh series of warnings about protecting yourself while outdoors.
Researchers have found the virus has already escaped into the wild, infecting feral pigs, so the virus is officially here to stay and cannot be eradicated.
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