Brisbane Lord Mayor Campbell Newman expects up to 20,000 houses and a further 2500 commercial properties will be flooded as water levels rise in the Queensland capital.
Thousands of people evacuated their properties on Wednesday afternoon as the Brisbane River hit the first of two predicted flood peaks.
Residents were being told that it was not too late to evacuate on Wednesday night.
Councillor Newman told residents: "Please, if the water's coming your way, it's not too late, you need to make a decision about evacuation or trying to sandbag."
"People shouldn't muck around. If they're on the flood map, if their street is on the list, make the decision to get out."
Homes and businesses were inundated in 35 suburbs as the river, swollen by water being discharged from the overloaded Wivenhoe Dam, hit a peak of around 4.5 metres.
The next peak will be around 4am (AEST) on Thursday when the waters are expected to reach around 5.2 metres, just below the 5.45 metres reached by the 1974 floods.
The Brisbane River is a swirling torrent with boats, pontoons and other debris being swept towards the sea and muddy water inundating low lying areas reports the ABC.
The city's ferry services have been substantially destroyed and could be out of action for months.
Raw sewage is spilling into the floodwaters after treatment plants were inundated by rising waters.
Authorities warn of a growing risk of disease, including Ross River Fever, hepatitis and gastroenteritis, as the floods linger into the weekend.
Brisbane's CBD was a ghost town on Wednesday with sandbags lining some shops and businesses.
The Port of Brisbane is closed.
The death toll from the flash floods in Toowoomba and the Lockyer Valley on Monday has now risen to 12, with 51 people still missing.
3000 homes flooded in Ipswich
Three thousand homes in Ipswich, west of Brisbane, are already submerged by floodwaters, with about one-third of the city affected.
The Bremer River, which runs through Ipswich, was expected to peak at 22 metres, but that has been revised down to 20.5 metres.
The 1974 flood reached a peak of 20.6 metres in Ipswich: 1800 premises were flooded and 41 houses were washed away.
More than 100,000 people were without power across the region as the power company cut supplies in low-lying areas.
Queensland Premier Anna Bligh says there were 3585 people in 57 evacuation centres in Brisbane and Ipswich and thousands more will be staying with relatives and friends.
She says she expects the total number of people in evacuation centres to rise to up to 6000 over the next few days.
Conditions similar to 1974
Conditions are described as similar to when Brisbane was hit by fatal floods on Australia Day weekend after Cyclone Wanda in 1974. Fourteen people died and almost 6000 houses were flooded.
Brisbane is Australia's third largest city, with a population of two million people.
Disaster declarations have been issued for the Brisbane, Bundaberg, Dalby, Gladstone, Gold Coast, Gympie, Ipswich, Logan, Maryborough, Rockhampton, Roma, Sunshine Coast, Toowoomba, Warwick and Redcliffe districts.
Ms Bligh says many regional centres are also facing serious flooding for the second or third time.
However, the 1974 flood in Brisbane was not the city's worst.
Figures from the Bureau of Meteorology listed by the BBC show the Brisbane River rose to 8.3 metres in 1893. An earlier flood was measured at 8.4 metres in 1841.