An evacuation order was issued for parts of the Goulburn Valley town of Seymour, in central Victoria, shortly before noon on Monday, before similar orders were put in place for sections of nearby Yea.
An emergency evacuation order was issued for the northern Victorian town of Rochester on Monday evening.
About 30 homes in Goornong, about 30km north-east of Bendigo, and six homes in Redesdale have been evacuated after water inundated the properties.
Emergency services said the rain was expected to move to Shepparton and Wangaratta midweek.
Victoria's emergency management commissioner, Rick Nugent, said there had been a record amount of rainfall in the past 24 hours to Monday afternoon.
"There were over three months of rain recorded in Heathcote in a 24-hour period," he said.
Nugent warned people in at-risk areas to have a flood plan.
He said emergency services rescued 38 people affected by the flooding, including some whose homes were inundated. But most were people attempting to drive through flood waters.
Tim Wiebusch, the chief officer of operations at the Victorian State Emergency Service, urged people not to drive through flood waters.
The Coomera river is seen cutting Clagiraba Road on the Gold Coast after heavy rains.
"It only takes 15 centimetres for a small car to float in flood waters," he said. "That's the height of an average pen."
Wiebusch said volunteers had responded to more than 1,200 calls for help since 7am on Sunday.
Relief centres have been set up in Bendigo, Seymour and Yea, and one will be set up in Echuca.
Flash flooding occurred in the state's south-west, while more than 180mm of rain was recorded in the central Victoria towns of Heathcote and Redesdale.
The premier, Jacinta Allan, said Redesdale recorded its "largest ever rainfall on record".
"We're still within that first 24 hour period of this emergency event, which means it's still in that immediate emergency response phase," she said.
Allan said an emergency cabinet meeting had also been scheduled for Monday night, to help plan the next phase of the flood response.
But she said it the weather event appeared to be "not as severe" as the 2022 floods that hit the same region and inundated thousands of homes and isolated many others, leading to a declaration of a state of disaster.
Heathcote, in the Macedon Ranges, recorded three months' worth of rain in 24 hours, Nugent said.
The persistent rain continued to defy predictions of a dry El Niño summer, with downpours that began late on Saturday and ramped up through Sunday and into Monday morning.
There were 920 calls for assistance to the State Emergency Service in 24 hours due to flooding, fallen trees and building damage.
The rain band mostly hit central Victoria and parts of inland New South Wales, senior BoM meteorologist Miriam Bradbury said.
"It is a really extensive range, extending through all of those states," she said.
On Monday morning, the NSW SES's spokesperson Brett Koschel said three storm crews and two flood rescue teams had been brought to the state's south from elsewhere on Sunday to assist if necessary.
"In the last 24 hours we've been making preparations for the forecast weather," he said.
"We've had some community members out there preparing their properties, and had those requests for sandbags so they've been able to prepare their properties as best they can."
In South Australia, the Bureau of Meteorology said thunderstorms continued to move to the state's south and east on Sunday and were forecast to head towards eastern border districts on Monday.
Rain would contract towards the east coast, bringing severe storm risk to Sydney and the Illawarra and Newcastle areas on Tuesday. That is forecast to continue north-east into Queensland through Wednesday and Thursday.
"That is good news for Victoria and southern NSW because [they] will start to see patchy showers and clear skies through Tuesday and Wednesday," Bradbury said.
- with Benita Kolovos
I wouldn't put much credence on their predictions, computer models or theories.