Many rivers in Victoria, including the Maribyrnong in Melbourne's west and the Goulburn further north, reached major flood levels, prompting the nighttime evacuation of residents.
"It's far from over, we'll see waters rise," Victoria Premier Daniel Andrews told the ABC.
"We'll see more and more waters continuing to rise, more and more houses being inundated, more and more communities being closed off."
Andrews said the state's purpose-built COVID-19 quarantine facility, closed last week after Australia scrapped isolation rules, could be reopened to shelter flood-impacted residents.
Though heavy rains are expected to ease from late Friday, flooding could continue through the weekend, officials said.