The $13.4 million in funding, announced on Thursday, will ensure the state's worst-affected public health units are supported for the next three months.
The state government also announced $6.5 million for health protection measures, including free Japanese encephalitis vaccines for people in flooded regions.
A dedicated system will also be set up to monitor and control disease-carrying mosquitoes.
The relief measures come as towns along the Murray River remain on high alert for severe flooding.
Residents in the northern Victorian town of Kerang have been warned it is too late to leave, after Patchell Bridge on the Murray Valley Highway was closed on Wednesday night.
Evacuation warnings are still in place for Echuca and the smaller towns of Barmah, Lower Moira and Bunbartha, with swollen rivers threatening to burst their banks.
In Echuca, locals have spent days building a two-kilometre makeshift flood levee through the town to protect thousands of homes and businesses.
On Thursday, the federal government announced an increase of 500 Australian Defence Force personnel to help with recovery efforts across Victoria and parts of NSW.
In Victoria, up to 400 ADF personnel will assist with various tasks, including sandbag distribution and doorknocking. The remaining ADF members will help out in NSW.
"We've already seen our ADF members hard at work filling sandbags in Shepparton, building levee banks in Echuca, and helping out in Wagga Wagga," Prime Minister Anthony Albanese said.
"Now they will also be supporting more people as we move to the clean-up phase of this disaster."
Federal Emergency Management Minister Murray Watt said the extra assistance would help some of the nation's hardest-hit communities.
An emergency warning was issued in Rochester on Thursday morning, alerting evacuated residents that it was not safe to return.
The Murray River is expected to peak on Friday, with concerns it could break the 1993 flood record and reach 95 metres.
Forecast thunderstorms and rain, with falls of up to 30mm, are expected for parts of north central and northeast Victoria from Friday.
Authorities are urging residents to heed the warnings after a second person was found dead in floodwaters.
The 65-year-old man's body was found at Nathalia, near Shepparton, on Wednesday morning.
His death follows that of a 71-year-old Rochester man on Saturday.
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