Emergency evacuation orders were in force on Saturday morning for Charlton Township at the foothills of the Great Dividing Range, Orrvale near Shepparton and the northeastern town of Wangaratta for properties within the Parfitt Road Levee System.
The evacuation order said major flooding was occurring on the Ovens River at Wangaratta, where the river was expected to reach 12.8 metres.
Shepparton in central Victoria is expected to experience its worst flooding in almost three decades from Sunday and residents have been told to prepare to evacuate.
It is now too late to leave the towns of Murchison and Murchison East, which are downstream of Shepparton along the Goulburn River.
As of 10am on Saturday there were major flood warnings for parts of the Avoca River, Goulburn River, King River, Mt Emu Creek, Loddon Weir, Ovens River, Broken River and Seven Creeks.
The extent of the damage to hundreds of home in the inner Melbourne suburb of Maribyrnong is just starting to become clear after the Maribyrnong River breached its banks on Friday.
Member for Maribyrnong Bill Shorten said many houses and a lot of community infrastructure had been damaged.
"I think that people here knew the theory of flood damage, but because it hasn't happened in a couple of generations of this significance I think it's a shock," Mr Shorten told ABC News.
People displaced by the floods are eligible for one-off payments of $560 per adult and $280 per child.
The federal and state governments have agreed to use the recently retired $580 million Mickleham quarantine facility as emergency accommodation.
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.
Mostly dry conditions were forecast for Monday and Tuesday across Victoria, but flooding is expected to return late in the week.
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