Torrential rain has affected regional and metropolitan areas alike, while authorities warn sodden catchments will mean weeks of flood risk.
The federal and state governments agreed on Friday to use the $580 million Mickleham quarantine facility as emergency accommodation a week after it was officially closed.
The facility will reopen early next week for 250 people with crisis accommodation available for six to eight weeks but its actual use will depend on demand, the Victorian government confirmed.
Evacuation orders are in place for Skinners Flat near Wedderburn, low-lying parts of Benalla on the Broken River gateway, Murchison along the Goulburn River, southwest of Shepparton, Maribyrnong in Melbourne and the town of Charlton at the foothills of the Great Dividing Range.
The Avoca River at Charlton is forecast to peak on Saturday afternoon, with the SES expecting flooding to be similar to 2010, when 40 properties were affected.
A dam failure at the Skinners Flat Reservoir in the Victorian goldfields was likely to bring nearly a metre of strong, fast-moving waters through the Wedderburn township, authorities warned.
About 70 residents were told to leave Maribyrnong in Melbourne, where a fresh evacuation order was issued on Friday afternoon after morning flooding.
An emergency alert for residents of Rochester along the Campaspe River to evacuate immediately is in place, with about 1000 properties expected to be inundated or isolated.
Many in Rochester sandbagged their properties and left town but some stayed to protect their businesses, motel owner Meagan Keating said on Friday afternoon.
"The anxiety is high … (because) as quick as the water is moving, it is a slow process, watching it come," she said.
At 3.30pm Friday, the SES had responded to more than 1850 requests for help in 24 hours and rescued at least 200 people across the state in two days.
One person was reported missing in central Victoria on Friday but police later announced a man was rescued after he ignored a roadblock and drove into floodwaters at Newbridge.
His vehicle was washed downstream and he managed to climb on to a tree branch, police said.
Officers rescued another woman in her 70s trapped in floodwaters near Newstead along the Loddon River and a man in a woman in a truck who became stranded trying to cross the Moorabool River at Maude.
Complacency has been blamed for the number of rescues.
Premier Daniel Andrews announced one-off payments of $560 per adult and $280 per child for people displaced by the floods.
About 1500 applications had been made by Friday afternoon.
Emergency relief centres have been set up near flood-affected areas.
Opposition Leader Matthew Guy called on the government to declare a state of emergency.
The Victorian Farmers Federation said the state government should work with its federal counterparts and declare a natural disaster in flood-affected areas.
The federal member for Maribyrnong, Bill Shorten, said the situation in the area he had called home for 30 years was devastating.
"The last big floods were in 1974, so for a lot of people this would be a new and devastating experience," Mr Shorten told reporters.
Traffic was disrupted across the state, while regional V/Line trains and replacement buses were cancelled on the Shepparton, Seymour, Albury, Echuca and Swan Hill lines.
The historical town of Seymour, 100km north of Melbourne, is facing its highest flood level since 1974.
Authorities also expect Shepparton in the Goulburn Valley to experience its worst flood in decades after the Goulburn River peaks on Tuesday.
