Queensland police warned that the Logan River, which runs through Beenleigh south of Brisbane, would only hit peak flood levels during the afternoon while further north the city of Rockhampton was also facing a serious threat.
Commissioner Ian Stewart warned there was "still a major risk to the community around Logan and further south caused by that flooding situation."
Rockhampton, with a population of over 80,000 on the Fitzroy River, was expected to suffer flood levels not seen for a century and Stewart urged residents in low-lying areas to leave.
"By Wednesday, we will be at peak flooding in Rockhampton," he said.
"It will be a gradual rise, so I encourage people to move now."
Queensland police tweeted "we currently have four people missing... that we have serious concerns about," including a 77-year-old man.
Tens of thousands of people have been evacuated from a string of towns in Queensland and New South Wales as the floods move south towards Ballina, cutting roads.
Others have tried to stick it out to save their properties.
The scene was grim along the Logan river.
Casey Bently, a 47-year-old mechanic from North Maclean appeared visibly upset as she looked at her house, submerged to the roof.
"We got as much out as we could in the short time that we had," she told AFP.
"People have lost everything. I'd only just finished renovating the house, and it is all gone again now."
Nearby a calf was stuck in a tree as a man in a kayak paddled out to see if it was alive. Dozens gathered to watch but by the time two people on jet skis arrived to help the calf only to discover it was dead.
'Very dangerous time'
"In many parts of the country you will see floodwaters continuing to rise over the next days," he told reporters.
"This is a very dangerous time in these flooded areas.
"I want to say to everybody who is affected by these floods - do not go into flooded waters. Do not cross flooded roads."
Category four Cyclone Debbie hit northeastern Australia on Tuesday between Bowen and Airlie Beach ripping up trees and causing widespread damage that is still being assessed.
It was downgraded to a tropical low as it tracked southeast still packing high winds and dumping huge amounts of rain all down the east coast to Sydney and beyond before blowing out over the Tasman Sea.
Police on Friday found the body of a woman who disappeared in floodwaters near Murwillumbah just south of the Queensland border.
And a 64-year-old woman, whose vehicle was swept off a causeway on a property in Gungal, in the Hunter Valley south of Sydney was also found dead Friday.
Lismore, south of Murwillumbah was among the worst flooded towns on Friday with Tweed Heads, Kingscliff and Murwillumbah also subject to evacuation orders.
In areas further north where the cyclone made landfall, water and power were still being restored.
Bowen, Mackay and the Whitsunday islands bore the brunt of the cyclone and nearly 40,000 homes were waiting to be re-connected on Saturday.
The military has mobilised 1,300 soldiers for the clean-up with helicopters and planes deploying to restore infrastructure and supply emergency food, water and fuel.
The Insurance Council of Australia declared the Queensland and northern NSW regions disaster zones, adding that the damage bill could top Aus$1 billion (US $770 million).
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