Japanese encephalitis, a flavivirus related to dengue and yellow fever, was detected in a resident in the state's north, the Department of Health announced on Tuesday.
The virus has also been picked up by environmental surveillance in northern Victoria along the Murray River, and in mosquitoes and feral pigs in NSW.
The disease is transmitted by mosquitoes and most people do not become sick but symptoms can include a fever, vomiting and headaches.
In more severe cases patients can experience seizures, paralysis, permanent disability or even death.
Victoria's Acting Chief Health Office Christian McGrath issued the alert and warned those near the Murray River or adjacent regions to take extra precautions.
These include using repellent on exposed skin and wearing long, loose fitting clothing when outside, and ensuring accommodation, including tents are properly fitted with nets.
"The risk of mosquito-borne diseases remains high in the coming weeks. Taking measures to avoid mosquito bites is critical to protect against infections," Dr McGrath said.
Recent findings indicate that Japanese encephalitis (JE) virus is likely circulating in northern Victoria— Victorian Department of Health (@VicGovDH) JE virus can cause a rare but potentially serious infection of the brain and is spread to humans through bites from infected mosquitoesMore: https://t.co/Yy0srPsSwJ1/4🧵 pic.twitter.com/EBN2Xv2BscDecember 31, 2024
It comes after a public plea was issued in Queensland last week after wet weather created ideal mosquito breeding conditions, increasing the risk of Japanese encephalitis spreading from NSW.
More than 50 NSW local government areas had been identified at "higher risk" of the virus, with it also detected in routine mosquito surveillance in the northwest Riverina region.
Risk of infection increases in the warmer months from November to March due to a higher number of mosquitoes.
Children aged under five and older people who are infected with the virus are at a higher risk of developing more severe illness, such as encephalitis
Mosquito testing is being carried out over the summer period to help identify high risk areas.