Queensland Premier Annastacia Palaszczuk says there's been no reports of injuries after Nathan crossed the coast near Cape Flattery, in the far north, early on Friday as a category four.
She said aerial surveillance would continue throughout the day, but it appeared the communities of Cooktown and Hopevale, south of Cape Flattery, had escaped relatively unscathed.
Nathan has already been downgraded to a category three storm and could be nothing more than a tropical low by the end of the day.
But Ms Palaszczuk said the system was expected to head out over the gulf and re-intensify.
"This cyclone will cross the cape and then head towards the Northern Territory, and probably then re-intensify from a category one to a category two," she told reporters.
She said Queensland authorities were in contact with the Northern Territory, as Nathan headed west.
In the indigenous community of Hopevale, 480 homes are without power and a banana plantation that provides jobs for locals has lost 60 per cent of its trees.
But she says the mayors of Hopevale and Cooktown have reported little damage.
"Overall we have some very good news."
Ms Palaszczuk said a helicopter would fly over evacuated Lizard Island, off the coast north of Cape Flattery, to assess damage.
Deputy Police Commissioner Steve Gollschewski said although there was no major damage on the mainland, residents shouldn't be complacent.
"There will be flooded roads. There will be winds," Mr Gollschewski said.
Bureau of Meteorology regional director Robb Webb said the strongest winds the bureau recorded were of category three strength at Cape Flattery, while measurements in Cooktown showed a category one level strength.
He said Nathan would re-intensify over the Gulf and could threaten the Northern Territory in two days' time.
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