Emergency services have had more than 8000 calls since the storm hit, and more than 58,000 homes and businesses have been left without power, which could take weeks to restore for some customers.
There are currently 11 flood warnings in place, with a major flood warning for the Traralgon Creek.
Other warnings have been issued for the Yarra and Thomson rivers.
Floodwaters are expected to rise in Traralgon today after consistent rain overnight, with an evacuation order in place for low-lying areas.
About 280 residents have been asked to leave their homes for a second time, after having had to flee on Thursday morning when the floods first hit.
At the moment, Traralgon Creek is at 2.87 metres and it is expected to hit the moderate flood level of four metres by this afternoon.
However, the Bureau of Meteorology has said the worst of the weather has probably now passed, bringing some relief for Victorians.
Emergency services have told Nine the clean-up could take months, with fallen trees currently blocking roads and isolating communities.
There are fears the storms could have also dealt a blow to Victoria’s COVID-19 vaccine rollout, with 2000 doses potentially lost due to power cuts.
The Health Department has said a batch of AstraZeneca doses is being assessed for their viability after power was lost at a vaccination site in Lilydale.