Ex-tropical cyclone Narelle weakened on Sunday after passing over remote Cape Shield in the Northern Territory's eastern Arnhem Land as a category-two system before 8am.
The weather system continued moving west throughout the day, packing wind gusts of up to 100km/h and bringing heavy rain as it shifted towards Western Australia.
Northern Territory Chief Minister Lia Finocchiaro said there were no early indications of major damage to infrastructure and no reports of injuries as the cyclone skirted population centres.
But the threat remained in the regional hub of Katherine, which she said was expected to see higher flood levels than those recorded after downpours a fortnight earlier.
"This is our seventh high risk weather event … the ground is saturated, our rivers are already full and any additional rainfall is going to make a significant impact," Ms Finocchiaro told reporters on Sunday.
Major flooding was expected in surrounding rivers on Monday after the storm's expected arrival on Sunday night.
Darwin was also included in a huge swathe of the territory covered by severe weather warnings.
Katherine mayor Joanne Holden said locals were prepared but stretched after the previous flooding, which was the worst in at least two decades.
"I think people are exhausted, both physically and emotionally," she told AAP.
"People have just gone through and cleaned out their damaged businesses and everything, and now here we are back sandbagging again."
An army of volunteers, with the help of Australian Defence Force personnel, worked to prepare the town.
The Bureau of Meteorology said the ex-cyclone was the first weather system in more than two decades that was expected to span three states or territories.
Narelle crossed Cape York in far-north Queensland on Friday as a category-four system, the second-highest classification.
The storm is due to move over the Joseph Bonaparte Gulf on Monday, potentially strengthening again to a category-two system with the potential to cause damage to homes.
Communities are also warned to expect abnormally high sea levels that could cause flooding of low-lying areas.
Flood warnings are in place across much of the Top End, including in the previously inundated community of Daly River.
Up to 30 patients, including nine pregnant women, were evacuated from Katherine Hospital in anticipation of ex-cyclone Narelle worsening the delicate flooding situation in the town.
Warnings are also in place for large swathes of WA.
People across the Kimberley have been told to prepare for the likelihood of heavy rain on Monday.
Disaster assistance payments of up to $1500 per family are being rolled out across the Northern Territory for those already impacted by the storm.
In Queensland, the clean-up from the cyclone continues with energy crews working to restore power to homes.
Police have delivered fuel to remote communities on Cape York to help locals recover from the storm, which brought down trees and ripped off roofs as it passed.
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