About 5,000 State Emergency Service volunteers are standing by, as experts warn of more than 250mm of rain falling across some parts of the state across the three days.
He warned Victorians not to become complacent and to check on neighbours and loved ones with more heavy falls to come on Friday night and into Saturday.
'This event will turn farms into lakes with such rapid rain rates'. Inner Melbourne had between 10 and 15 millimeters of rain by about 5pm on Friday, and the outer suburbs had between 20 and 40 millimeters.
A flood watch has been issued for rivers across the state, including Melbourne's Yarra River, with widespread flooding likely from Friday onwards, the bureau says.
Asked if the worst was still to come, Mr Lapsley said: "absolutely".
A rain event of this forecasted magnitude hasn't been seen in metropolitan Melbourne since 2005 and in regional Victoria since 2010, SES deputy chief Tim Wiebusch said.
It only takes 15cm of water to float a vehicle, SES deputy chief Tim Wiebusch warned.
Mr Williams said on a scale of one to 10, he'll "take a punt and say it's a 10 for Victoria".
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It was not immediately clear how many people were wounded, with reports varying from at least five to 11 people. The number of residents present at the hostel is unclear, but an operation is underway to safely recover them.
Authorities have also urged people to stay home and avoid travel if possible.
Parts of Melbourne's north, including Pascoe Vale, saw flash flooding on Friday.
After record breaking heat through Victoria this month, on Friday alone, Melbourne could receive its entire December rainfall average and potentially the entire summer's worth by Sunday.
"Half the inhabitants of Melbourne have probably never seen something like this", Mr Williams said.
Unharvested crops are at risk of being wiped out, with farmers in some parts of the state working around the clock since Wednesday to finish harvesting.
"With some common sense and looking out for each other, I know Victorians will get through this very hard period", Andrews told reporters in Melbourne on Friday afternoon, as he urged people to leave work early.
Severe winds and heavy rain are predicted to roll across South Australia.
The storms will develop in the far west late on Thursday before extending across the rest of the state on Friday.