In Victoria's northwest, 12 homes were inundated at Creswick and four homes were flooded above floor level in Delacombe, near Ballarat.
Ballarat region Incident controller Stephen Walls said up to 25 people are at a Stawell relief centre after they had to be evacuated from their homes in Halls Gap.
The Bureau of Meteorology (BoM) has forecast more rain on Saturday across Victoria, particularly in the state's northeast which is expected to receive up to 100mm of rain.
Elsewhere across the north, northwest, central and west and south Gippsland areas of Victoria, up to 50mm is likely.
Metropolitan Melbourne is set to receive up to a further 50mm of rain on Saturday.
The heavy rain has also fallen on catchments already saturated by the December and January rain events. The BoM has a major flood warning for the Loddon River, moderate flood warnings for the Kiewa, Mitta Mitta Rivers in the northeast as well as Dandenong Creek.
Minor flood warnings have been issued for the Yarra River, Avoca River Broken River and the Werribee River upstream from Lake Melton.
There are also several major roads closed due to flooding including parts of the Princes Freeway and the Maroondah and Calder Highway.
There were also several closures of train lines in Melbourne which included the Williamstown, South Yarra and Sandringham lines.
State Emergency Service state controller Trevor White also urged residents to continue to keep a watch on local conditions, be prepared for further flooding activity and stay off roads if possible.
"We are asking Victorians to avoid travelling by road if possible and please never drive, ride or walk through floodwaters - this is the main cause of injury and death during flood emergencies," Mr White said.
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