Tropical Cyclone Narelle was upgraded on Thursday to a powerful category four system off the Western Australian northwest coast.
The storm is on track to make landfall late on Friday in the Shark Bay area as a category three system, which can produce gusts up to 224km/h.
Tourists have been told to leave the region, major roads have been closed, and evacuation centres have been set up ahead of Narelle's arrival.
Shark Bay shire president Peter Stubberfield said volunteers were busy sandbagging ahead of a possible tidal surge in the tiny holiday town of Denham on the Peron Peninsula, 830km north of Perth.
"We're preparing for the worst, which could be a category three cyclone, and we're hoping for anything less than that," he said.
Mr Stubberfield said tourists had been asked to leave the community of about 700 people, which has one road into it from the mainland, but some were refusing.
"There seems to be a bit of pushback for some people; some of the travellers don't seem to be taking it seriously, which is a bit frustrating," he said.
Narelle's epic journey across northern Australia began when it made landfall in Queensland as a category four system on Friday, crossing the Cape York Peninsula.
It left a trail of power outages and flooding as it hit the NT as a category three by Sunday, forcing hundreds of people to evacuate.
After initially crossing northern WA as a tropical low on Monday, Narelle has gained strength in the Indian Ocean, as it headed southwest along the Pilbara coastline.
It is producing gusts up to 230km/h and is located about 365km northeast of Exmouth.
Tackle shop manager Barry Taylor said Exmouth residents had been hard at work "getting everything as locked down or strapped up and as safe as we can" ahead of Narelle's arrival.
"Fingers crossed we don't cop it too hard," he said.
The system is set to move southeast after crossing the coast and pass as a tropical low east of Perth on Saturday, bringing showers and thunderstorms.
More than a week after arriving, Narelle is expected to finally leave Australia when it moves into the Southern Ocean early on Sunday.
Some homes in the NT town of Katherine have been inundated for the second time in a month.
The Katherine River was expected to peak just above the major flood level of 17.5 metres at the town bridge on Thursday.
The river rise, caused by heavy rain dumped by Narelle, flooded streets in the town and put water through low-lying properties, including on Gorge Road and in the nearby community of Kalano, mayor Joanna Holden told AAP.
Emergency shelters have been prepared to take evacuees and a portable field hospital has been set up after the town's hospital was closed.
Homes and businesses in Katherine were inundated on March 7 after the river peaked at 19.2 metres, causing the town's worst flooding in 28 years.
Ms Holden said the river was likely to sit at a major flood level of about 17.5 metres for some hours before receding.
It was too early to say if the worst of the new flooding was over, she said.
"Until that river drops right back down, any rain now is a risk."
Residents have had to put their clean-up on hold, but prepared for renewed flooding with a major sandbagging operation by volunteers and defence force personnel sent in to assist.
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