People in Tinamba, Tinamba West, Newry, Mewburn Park, Bellbird Corner and Riverslea near Maffra have been told to leave with flooding expected from 10pm on Wednesday.
An alert issued by Vic Emergency urged them to take their pets, mobile phones and medications, with the best evacuation route being Maffra-Sale Rd towards Sale.
A major flood warning has also been issued to residents along the Macalister River downstream of Lake Glenmaggie, with locals told to move to higher ground.
Total rainfall in that area was 150mm in the 24 hours to 9am on Wednesday and further rain was forecast into Thursday.
The river was at 5.75 metres and rising on Wednesday afternoon, with further planned releases from Lake Glenmaggie.
There were hundreds of calls for help as rivers continued to rise and damaging winds lashed the region following days of bushfire threats.
Most calls for assistance to the State Emergency Service overnight were connected to flooding near Eildon.
A farmer had to be rescued from floodwaters in Alexandra after he got into trouble attempting to rescue cattle on a tractor, police said.
Footage from the incident showed the vehicle stranded in gushing water metres away from what appeared to be a dirt road.
The 43-year-old Alexandra man suffered non-life-threatening injuries and was taken to hospital.
Fires at Briagolong and Loch Sport were downgraded to advice warnings with the focus firmly on areas at risk of flooding after the deluge on Tuesday and Wednesday.
Watch and act alerts for flooding were issued across eastern Victoria for as far north as the King River at Cheshunt and south to Glenmaggie.
Residents along the Acheron River near Marysville and the Goulburn River near Lake Eildon were warned moderate flooding was expected after 140mm of rain fell in 24 hours.
An alert was also issued for parts of the Yarra River on the outskirts of Melbourne.
Emergency Services Minister Jaclyn Symes said the situation was dynamic.
"We have, in good news, downgraded emergency warnings for fire," Ms Symes told reporters at state parliament.
"We've had a lot of rain across the state and that has brought flood concerns and flash flooding concerns."
The Bureau of Meteorology placed Melbourne and most of the state's east under flood watch with more rain expected throughout Wednesday.
Energy Minister Lily D'Ambrosio said she was working closely with providers to ensure the wild weather and natural disasters had a minimal impact on energy supply.
Conditions were expected to ease from Thursday but flooding was tipped to last until the weekend.
The flood threat came after many residents in Gippsland were put on alert for fires.
About 700 firefighters spent three days battling two blazes, with one home lost in Briagolong but no reports of serious injury.
The cause of that blaze, which burnt about 17,500 hectares, is under investigation.
10°C