The Bureau of Meteorology warned storms would sweep across Melbourne from Victoria's west, with peak thunderstorm activity to hit the city between early and mid-afternoon on Friday.

A severe weather warning was issued for damaging winds, heavy rainfall and flash flooding to include Melbourne, Frankston, Bacchus Marsh, Rosebud, Ballarat and Geelong.

"A cluster of strong storms continues to move eastward in a very humid environment and is expected to produce heavy rainfall and damaging winds. Isolated destructive wind gusts are possible," the BOM alert said.

Later on Friday the severe weather warning for Greater Melbourne was lifted, but authorities said more storms could hit overnight into Saturday.

Geelong, Cape Otway and the Surf Coast were battered by heavy rain on Thursday evening, with 40 to 70mm of rain recorded around Geelong.

State Emergency Service volunteers have received hundreds of calls for help through Friday as homes, buildings and roads were flooded.

Late on Friday a severe thunderstorm alert was issued for Shepparton, Wangaratta, Mansfield and surrounds, with people told to watch and act and take shelter.

"Life-threatening flash floods" could occur in areas including Euroa, Wangaratta, Mansfield and Mount Buller, emergency services warned.

Flash flooding hit Werribee, in Melbourne's west, Ballarat and the Brisbane Ranges.

In Melbourne several people were rescued from cars despite warnings for motorists not to drive into floodwaters.

Thousands of Victorians remained without power late on Friday.

Australian Associated Press