Murray Valley encephalitis and Kunjin virus have been detected in Western Australia's Kimberley and Pilbara regions for the first time this year.
No human cases of infection have been reported in 2014 so far, but the viruses have been picked up in sentinel chicken flocks, which are used as an early warning system.
Department of Health entomologist Peter Neville says residents and travellers in the Pilbara and Kimberley should take precautions to avoid mosquito bites, which is how the viruses are carried.
While the risk of being infected and becoming unwell is low, the illnesses can be severe and even fatal.
Initial symptoms of Murray Valley encephalitis include fever, drowsiness, headache, stiff neck, nausea and dizziness.
In severe cases, people may experience fits and lapse into a coma, and may be left with permanent brain damage or die.
"In young children, fever might be the only early sign, so parents should see their doctor if concerned, particularly if their child experiences drowsiness, floppiness, irritability, poor feeding, or general distress," Dr Neville said.
Kunjin virus usually causes milder symptoms, but in rare cases may lead to delirium and coma.
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