Some residents in Greater Shepparton, Strathbogie, Moira, Benalla, Campaspe and Gannawarra local government areas will continue to be eligible for the vaccine.
The call for at-risk communities to be vaccinated against the JE virus comes as the Department of Health launches a new campaign warning of the risks of mosquito-borne diseases.
People should get vaccinated ahead of summer, which brings an increased mosquito presence.
Vaccination against JE is available for people who live or work in 20 local government areas considered at higher risk of JE virus infection.
It is available for those who live or routinely work in any of the high-risk government areas and regularly spend time in outdoor activities that place them at risk of mosquito bites, are homeless, or are living in conditions with limited mosquito protection such as tents, caravans, or houses with no insect screens.
The vaccine is free and available from GPs, Aboriginal community-controlled organisations, community pharmacies and local councils.
Most people with Japanese Encephalitis virus infection do not show or have only mild symptoms, but in extreme cases, it may lead to death or permanent disability.
Symptoms usually develop five to 15 days after being bitten by an infected mosquito.
They include fever, headaches and vomiting.
Symptoms for severe infections can include severe headaches, neck or back stiffness, sensitivity to light, confusion, seizures, paralysis and comas.
The risk of infection from mosquito bites rises usually between November and March when there is an increased number of mosquitoes.
For more information about the disease, visit health.vic.gov.au/infectious-diseases/japanese-encephalitis
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