Evacuation 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 hundreds in the city of Benalla on the Broken River and Wedderburn following a breach at Skinners Flat Reservoir.
Strong, fast-moving water from the dam a metre deep was expected to course through Wedderburn township via the Calder Highway, authorities said on Friday morning.
The State Emergency Service has carried out 108 flood rescues in the past 48 hours.
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 ABC Radio on Friday.
"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."
Officials have responded to 2660 requests for help in the past 24 hours.
No flood-related injuries or deaths have been reported.
Mr Gamble said about 500 homes were flooded and another 500 had been isolated, with about 3500 properties without power.
Premier Daniel Andrews announced one-off payments of $560 per adult and $280 per child for people displaced by the floods.
The payments 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," Mr Andrews told ABC Radio.
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 and Seymour.
Prime Minister Anthony Albanese has spoken to the premier about potentially standing up the Mickleham quarantine facility as emergency accommodation a week after it was officially closed.
Those 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 due to flood-related impacts.
Watch and act alerts urging people to stay indoors are widespread across Victoria.
Areas north of the Great Dividing Range were among the heaviest hit by the rain through Wednesday and Thursday and more central areas also saw significant falls, according to the Bureau of Meteorology.
Between 9am and 6pm on Thursday, Pyalong recorded 62 millimetres and Avalon Station had 60mm.
While Strathbogie North also recorded a 58mm dump on Thursday after copping 187mm since Wednesday morning.
The big wet started to clear out of western Victoria on Thursday night and forecasters predict conditions will improve for the state's central parts and then into the east on Friday.
Seymour faced its highest flood level since 1974.
Authorities also expect Shepparton to experience its worst flood in almost three decades on Saturday afternoon.
