Tropical Cyclone Fina, which rampaged across the Northern Territory, all but flattened the Berkeley River Lodge as it crossed the Western Australian coast on Monday night as a category 3 system.
The exclusive resort, which can only be reached by sea or air, sustained extensive damage to its accommodation villas and infrastructure.
"The property has sustained significant damage," owner Chris Banson said on Tuesday.
"Importantly, our two on-site caretakers are safe."
Fina completely destroyed three of 18 villas and damaged others, along with the resort's central lodge and staff accommodation.
"Water and power services are no longer operating (and the) surrounding vegetation has also been impacted," Mr Banson said.
No guests were at the resort, which is described as offering "barefoot luxury in one of the planet's most untouched frontiers" on its website.
Photos of the damaged resort show a villa toppled on its side, debris strewn across the coastal landscape and trees stripped of their leaves.
The Department of Fire and Emergency Services will evacuate the pair, who were among only four people in the cyclone warning area when it crossed the coast, when it is safe to do so.
Fina has since been downgraded from a category one system to a tropical low as it tracks southwest through WA's north.
On Tuesday afternoon WA time it was located about 115 kilometres northwest of the town of Wyndham, the Bureau of Meteorology said.
A severe weather warning has been issued in the region for heavy rainfall, flash flooding and large tides and waves.
Wind gusts up to 85km/h and six-hourly rainfall totals up to 200mm are possible.
In the NT, where power was cut to about 17,000 homes and properties, PowerWater said 85 per cent of customers had been reconnected and work continued to restore the remaining 3000 that remained without it.
The NT government has also announced it will make $250 disaster recovery hardship payment available to those impacted by the cyclone on Wednesday.
The Tiwi Islands, north of Darwin, were among the areas hardest hit, with power cut, trees felled and a school closed.
Tiwi College on Melville Island has been shut until further notice after suffering significant structural damage, with school staff reportedly evacuated after some buildings lost their roof.
Ceilings caved in and a tree damaged a school water tank but no one was injured in the storm.
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