The State Emergency Service (SES) is expecting floodwaters to recede slowly south-east of Melbourne this evening, but homes still remain at risk of isolation.
More residents in Koo Wee Rup and nearby communities have been door knocked, to let them know their homes are at risk of becoming isolated if the high tide picks up on the Bunyip River.
The current flooding is being partially blamed on a problem with Koo Wee Rup's drainage system.
Many people left their homes last night as 60 millimetres of rain drenched the region.
But Lachlan Quick of the SES says the rain has eased and floodwaters are likely to recede.
"The other challenge is if it's actually gone over banks [it] can't actually recede that quickly," he said.
"It does have to go back through the drainage system again."
The SES says two homes have water over the floorboards but many more are surrounded by floodwaters.
The water is now expected to recede, but Mr Quick says more flooding could be on its way over the next few months.
"For the, certainly Gippsland area and certainly the north-east have already had quite a lot of rain," he said.
The Cardinia Shire's Myles O'Reilly says a flood emergency centre has been set up in Packenham.
Resident David Vandehoef says he has never seen such flooding.
"It came as a bit of a surprise really," he said.
"I think the house down the corner there is under water."
© ABC 2012
08:08 EST An amazing video shows an Oklahoma tornado survivor being reunited with her dog when it is found in the rubble of her flattened house as she is being interviewed on US television.