One home has been flooded and more than 40 remain on alert as floodwater inundates areas southeast of Melbourne.
Emergency crews advised residents in 44 homes in Koo Wee Rup to evacuate about 4am (AEST) on Friday as flood waters from days of heavy rain and a high tide spread through low-lying areas.
SES spokeswoman Dimity York said just four of the 44 properties chose to evacuate, with two going to a relief centre and two to the homes of family or friends.
Ms Dimity said one house has been flooded. It is unoccupied.
Despite the flooding, Ms York said there had been just eight calls for help in Koo Wee Rup.
Several roads in the region are under water and closed.
In metropolitan Melbourne, the SES received 81 calls for help since midnight, including one to rescue a person stuck in their car in flood waters.
Most calls were because of leaking roofs and flash flooding in streets and backyards.

