UP to 25 patients were evacuated from an aged care facility in Rushworth in the state's north east on Wednesday night after heavy rainfall caused flash flooding across the region.
Strong winds also caused damage to the roof of the town's IGA supermarket, said SES spokesman Toby Borella.
He said the SES had received 124 calls since 5pm mostly due to flash flooding and wind damage. About 70 of those calls came from residents in Shepparton and the surrounding area.
"Shepparton was probably the hardest hit so far," Mr Borella said. "In Shepparton alone, there's been five requests for persons that have been trapped in vehicles that have been driven into flood water."
Duty forecaster Geoff Feren from the Bureau of Meteorology said Shepparton had received 48mm of rain in the 12 hours to 9pm.
"Between 7.30 and 8pm they had 27mm of rain in half an hour which is exceptionally heavy rain."
He said: "There is still severe thunderstorm warnings and severe weather warnings for the heavy rain across much of the east of the state."
On Wednesday night, the CFA said significant rainfall on Wednesday had helped to contain a bushfire that has been burning out of control near Harrietville since January 21. A CFA spokeswoman said the Grampians fire had also been contained.