Tropical Cyclone Fina downed trees and cut power to thousands as it rampaged across the Northern Territory before crossing the coast into Western Australia as a category three system overnight.
Winds gusts in excess of 170 km/h battered parts of the Kimberley region near Berkeley River Mouth before weakening as it tracked southeast overland.
It's now a category one storm, with sustained winds near the cyclone's centre of 85 km/h and wind gusts to 120km/h, the Bureau of Meteorology says.
"It is expected to weaken further today while drifting slowly inland, and will transition from our tropical cyclone warning to a severe weather warning for heavy rainfall in that area this afternoon," a bureau spokesman told ABC Radio.
Flash flooding in the northeast Kimberley region is possible, with residents between King George River Mouth and the WA/NT border warned that high tides could rise above the normal mark.
The area inside the bureau's current cyclone warning zone is sparsely populated.
Just four people at Berkeley River Mouth and Faraway Bay were bunkering down, including in a buried sea container, when the weather system crossed the coast, WA Department of Emergency Services said.
Staff at Berkeley River Lodge made it through night unharmed but the remote luxury resort sustained significant damage with the "total loss of infrastructure at different levels", Superintendent Todd Pender told ABC Radio.
In the NT, a major clean-up is underway as crews work to restore power to thousands of homes and clear roads of debris.
The Tiwi Islands, north of Darwin, were among those 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.
Melville and Bathurst Island residents were still enduring outages on Tuesday.
Some homes may be without power for days after the cyclone brought destructive winds and heavy rain as it passed through on the weekend, intensifying into a category four en route to WA.
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