After crossing the WA coast early on Friday between De Grey and Pardoo as a category five system, Ilsa was downgraded to category one by afternoon as it tracked through the eastern Pilbara with wind gusts up to 170km/h.
Inland WA is being urged to remain vigilant as Ilsa continues to deliver destructive winds and flooding but the storm is expected to weaken below tropical cyclone strength as it moves into southern parts of the Northern Territory on Saturday.
Forecasters have warned communities including Alice Springs, Yulara and Ti Tree to be on alert for flash flooding and gale-force winds.
"Those really intense rainfalls are going to fall over a space of few hours so there could be some flash flooding through the area, particularly the northern parts of the Lasseter district and into the northwest parts of the Simpson Desert," senior meteorologist Sally Cutter said.
Meanwhile, a red alert remains for Wallal Downs on the WA coast and inland to Telfer, Punmu and Parnngurr.
"I wanted to just really emphasise for those communities, even though the system has crossed the coast, please remain vigilant," the Bureau of Meteorology's Todd Smith said on Friday.
Telfer gold mine operator Newcrest Mining has begun assessing the Pilbara site for hazards like fallen power lines and loose tree branches as well as any hidden structural damage.
"Pending inspections of the airstrip and village, we aim to commence bringing the majority of people back to site from tomorrow afternoon and through the remainder of the weekend," the miner said on Friday.
Pardoo Roadhouse and Tavern, 150km northeast of Port Hedland, bore the brunt of Ilsa as it made landfall, packing record winds of 213km/h.
"We are all still a bit shaken and emotional to see the damage," they posted on Facebook.
"She may have wiped us out but she can't take away our spirit."
The owners have launched a GoFundMe page to help pay for an estimated $4 million in damage.
"The roof of our roadhouse is gone, staff rooms and buildings have been wiped out, most of the accommodation we offered onsite has been wiped out or received extensive damage," they wrote.
WA Fire and Emergency Services Commissioner Darren Klemm said the full extent of the destruction may take days to be realised.
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