Heavy rain has flooded shops in Bendigo's CBD and damaged buildings.
The SES had more than 100 calls within an hour from Bendigo, mainly for water damage.
Bureau of Meteorology forecaster Stephen King said the intense rain had caused flash flooding in the Victorian city.
"I think they had up to about 15mm in 15 minutes," Mr King told AAP on Friday.
Staff at Bendigo's Myer store confirmed they had closed because of floods. Other shops also shut their doors due to the rain.
Part of a ceiling fell in at a shopping centre at Kangaroo Flat.
Mr King said Bendigo could expect more rain overnight and through the weekend.
A severe thunderstorm warning has been issued for large parts of Victoria, along with heavy rain alerts.
"Now some of the thunderstorms are showing the possibility of hail and wind, so we've had to issue that warning," Mr King said.
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