Heavy rain, damaging winds and large hail are possible in eastern parts of the state over two days.
"We're going to see some potential flash flooding and severe thunderstorms over the next couple of days, including [in] some damaged fire areas," Emergency Services Minister Lisa Neville said.
She also told reporters up to 70 people were expected to fly back into the small town of Mallacoota, where bushfires trapped thousands on the beach.
"We're hoping tomorrow... 300 people want to fly back in and that'll be our first priority and we're looking at around 70 people to fly back in tomorrow," Ms Neville said.
She said people who were reuniting with family members that stayed in the stranded East Gippsland coastal town were the priority.
The government is also hoping to clear roads to the isolated community so people could access properties and vehicles abandoned due to the fires.
Downpour unlikely to put out Victoria fires
The weather bureau confirmed the state was about to be hit by downpours, but the rainfall would be "hit and miss" and unlikely to put out blazes.
"Victoria is about to see its wettest two-day period in many, many months," Bureau of Meteorology senior forecaster Dean Narramore said on Sunday.
The weekend also saw firefighters work to contain a blaze at French Island at Western Port which started on Saturday.
Severe Weather Warning remains current for much of central and eastern Victoria. Rain increasing in #Melbourne throughout the morning; heaviest during the afternoon and evening. https://t.co/HLs2UYFQyQ #melbweather pic.twitter.com/46KqbpKK9a— Bureau of Meteorology, Victoria (@BOM_Vic) January 19, 2020
An emergency warning was issued on Sunday evening for a bushfire in central Victoria threatening lives and homes in Pastoria.
It was later downgraded to a "watch and act" early on Monday.
Across the state, 396 homes have been destroyed in bushfires and more than 600 outbuildings including sheds have also been razed.
More than 223 blazes started in Victoria in the last week and of those, 20 were classed as "significant" and burned more than 50 hectares.
Do you have a story tip? Email: firstname.lastname@example.org.