Five hundred homes have flooded, another 500 have been isolated and about 9500 are without power across Victoria.
Torrential rain has impacted regional and metropolitan areas alike, while authorities warn sodden catchments will mean weeks of flood risk.
Evacuations orders are in place for the town of Rochester along the Campaspe River, north of Melbourne, the central goldfields town of Carisbrook near Maryborough and Seymour on the Goulburn River.
About 70 residents have been told to leave Maribyrnong in inner Melbourne, along with thousands in the city of Benalla on the Broken River and at Wedderburn following a breach at Skinners Flat Reservoir.
Strong, fast-moving water from the dam a metre deep was expected to course through the township via the Calder Highway, authorities said on Friday morning.
Victoria's Emergency Management Commissioner Andrew Crisp expects huge volumes of water to enter the Murray River in coming days as the deluge moves downstream from Victorian and NSW catchments.
"We will literally have weeks of this," he told ABC radio.
The State Emergency Service has responded to 2660 requests for help in 24 hours and carried out at least 120 flood rescues over the past two days.
State commander Josh Gamble said complacency was the main reason for people getting into trouble.
"That is quite significant and we haven't had that many flood rescues for quite some time, for some years in fact," he told the ABC.
"Many of these people are putting their own lives at risk, their own children in some circumstances, but more importantly, other community members and responders and that's in all parts of the state not just metropolitan areas."
Premier Daniel Andrews has announced one-off payments of $560 per adult and $280 per child for people displaced by the floods.
They can be claimed online from 9am AEDT on Friday.
"We'll put extra staff on and get those payments made as quickly as we can," he said.
Anglers Tavern, on the banks of Melbourne's Maribyrnong River, was partially submerged following the unprecedented overnight rain.
"At this stage we don't have access to it," a spokeswoman said.
"Obviously there has been flood damage to the venue and we'll assess that once we have access - hopefully tomorrow depending on the weather."
Opposition leader Matthew Guy has called on the government to declare a state of emergency.
The SES said the areas most under threat on Friday morning included Maribyrnong, Carisbrook, Seymour and Rochester.
Rochester residents were told to abandon homes with rapidly rising floodwaters likely to inundate the area and leave 700 properties isolated from early Friday.
The Campaspe River was slated to peak in the afternoon.
Emergency relief centres have been set up close to Rochester, Carisbrook, Seymour, Wedderburn and Maryborough.
Prime Minister Anthony Albanese has spoken to the premier about using the Mickleham quarantine facility as emergency accommodation a week after it was officially closed.
Residents along the Campaspe from Lake Eppalock to Barnadown have also been advised to get to higher ground, while an emergency warning has been issued for Seven Creeks to Euroa.
There have been traffic delays across Victoria due to road closures.
V/Line trains and replacement buses were cancelled on the Shepparton, Seymour, Albury, Echuca and Swan Hill lines.
The town of Seymour faced its highest flood level since 1974.
Authorities also expect Shepparton to experience its worst flood in almost three decades on Saturday afternoon.
