The floods, which have hit 75 towns across Victoria state and affected 1,770 properties, are estimated to cover an area 90 kilometres (56 miles) long and 40 kilometres wide, ABC radio reported.
"We know that this is the most significant flooding in the north west of Victoria since records began... about 130 years ago," a spokeswoman for the State Emergency Service told AFP.
"We are still on alert for towns in the north of the state."
Eastern Australia has been lashed by torrential rains triggered by La Nina, a weather system associated with cyclones, which caused massive floods that devastated Queensland and spread south to New South Wales.
After surging torrents of dirty brown water flooded an area the size of France and Germany combined in Queensland -- killing more than 30 people and leaving a massive trail of destruction -- more floods developed in Victoria.
Several small communities are now under threat as the waters move north towards the town of Swan Hill, some 300 kilometres northwest of Melbourne.
"In the actual Swan Hill township itself, we are very confident that the levee system around the town is built to a very high grade and will protect the township," Mayor Greg Cruickshank told ABC radio, which described the floods as an "inland sea".
"But most of our rural and outlying areas around Lake Boga and Pental Island and the Tyntynder Flats will have significant amount of inundation through them."
The nearby town of Kerang has already been cut off by the moving waters, while homes are at risk in Beulah and Jeparit.
"The Wimmera River going through Jeparit remains a pretty significant concern for us," SES spokesman Lachlan Quick said.
"The community has been notified and protection works have been undertaken."
As the recovery and clean-up continues in Queensland, the 75,000 residents of the northeastern city of Rockhampton, which was almost entirely isolated by floods earlier this month, are expected to soon have their air link back.
Some three weeks after Rockhampton airport's runway disappeared under water, day time flights will resume on Monday after all major repairs and fencing work has been completed, officials said.
"Due to extensive flood damage, the secondary runway will remain closed for an extended period," the airport said.