At least two people have died and around 20,000 more have been ordered to leave their homes after ex-Cyclone Debbie brought heavy rainfall and flooding to large parts of NSW.

In Queensland, residents in low-lying parts of Rockhampton have been warned to prepare for what could be the biggest flood to hit the area in almost a century.

Police Commissioner Ian Stewart has warned the Fitzroy River could reach 9.5 metres at Rockhampton on Friday, which would be the biggest flood to hit the city since 1918.

Stewart warned those in low-lying areas to start moving their property to higher ground on Saturday.

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"I'd encourage people to move now. Don't wait until Monday or Tuesday," he said today.

He said the Fitzroy is gradually rising and low-lying areas would begin to be cut off in the next couple of days.

The city's airport is also likely to be inundated by some time on Monday, while roads in and out of the city could also be cut.

At 9.5 metres, the peak could surpass the levels of the 2011, 1991 and 1954 floods.

It is expected homes in the Depot Hill area and low-lying parts of Berserker, Allenstown and Kawana will be inundated when the Fitzroy reaches the major flood level of 8.5 metres on Monday afternoon.

Additional emergency services personnel are being moved into city as the river rises.

Police currently hold serious concern for four people missing in flood-affected areas.

Major flooding has already been recorded in the Mackenzie, Connors and Isaac rivers that flow into the Fitzroy following heavy rainfall from ex-cyclone Debbie.

Minor flooding has also occurred upstream in the Fitzroy, and major flooding is expected in the Yaamba area, north of Rockhampton, on Monday.

The Wilson's River breached its banks flooding the far-northern NSW town of Lismore. Photo / AAP
The Wilson's River breached its banks flooding the far-northern NSW town of Lismore. Photo / AAP

Meanwhile, Prime Minister Malcolm Turnbull is urging flood-affected residents to be careful following the deaths of two women as waters sweep through northern NSW and southeast Queensland.

"This is a very dangerous time in these flooded areas," he told reporters in Melbourne today.

"The flooding that has followed is of a very, very dangerous scale in parts of southern Queensland, right through Queensland, and indeed in northern NSW."

While tropical cyclone Debbie has been downgraded, the risk of flooding remains.

"We've had two fatalities, two women in NSW have died as a result of these floods and our thoughts and prayers are with their families.

"This is going to be a tough time for them, but the important thing is everyone should stay safe."

Turnbull has urged residents to listen to the advice of authorities and emergency services.

"I want to say, everybody who is affected by these floods, do not go into these waters," the prime minister said, adding that the waters are expected to rise.

"If it's flooded, forget it."

Around 20,000 people in northern NSW were ordered to evacuate yesterday after ex-cyclone Debbie dumped heavy rain across large parts of the state's north.

"I want to thank the emergency services who, as they always do, show the very best of Australia and Australian spirit right at the time when nature flings its worst at us," Turnbull said.

The federal government says the Australian Defence Force has been helping affected areas in the biggest pre-deployment in advance of a natural disaster.


-AAP