Ross River virus infected 314 people in Victoria in 2016, nearly a 50% increase on the year before, said the state's chief health officer Charles Guest.
Prof Guest suggested stagnant water from recent heavy rain created conditions ripe for mosquito breeding.
The virus, found in Australia and some Pacific nations, can cause joint pain, fatigue and muscle aches.
Current treatments only target symptoms, which can last for months.
"The best protection from these diseases is to avoid mosquito bites," Prof Guest said in a statement.
