Residents in Port Hedland were told to seek shelter overnight as the cyclone crossed the Western Australian coast as a category-five system, but they emerged on Friday morning to find the town relatively unscathed.

Mayor Peter Carter said he was awake for most of the night, listening to howling winds when the wind and rain suddenly died about 1.30am.

"I was up most of the night, watching the trees, thinking here it comes, then all of a sudden it just died off," he told AAP.

"It had an eerie feel, really strange - Mother Nature does interesting things. We dodged a major bullet last night."

WA Department of Fire and Emergency Services incident controller Glenn Hall said initial inspections indicated Cyclone Island had not caused widespread damage in the town, home to about 16,000 people.

Mr Carter expected the port would be up and running within 12 hours and the mines would be operating again by nightfall.

The tropical cyclone crossed the Western Australian coast as a category-five system between De Grey and Pardoo about midnight on Thursday, bringing winds of 213km/h.

It was later downgraded to a category-three system as it travelled hundreds of kilometres inland towards Telfer, Punmu and Kunawarritji.

The eye of the cyclone passed close to the iconic Pardoo Roadhouse and staff posted on Facebook that the property had "suffered great damage."

"We are all still a bit shaken and emotional to see the damage from Cyclone Ilsa," a post said.

"She may have wiped us out, but she can't take away our spirit. We face a massive clean-up with plans to rebuild."

The Bureau of Meteorology's Dean Narramore said Cyclone Ilsa might have delivered a new record for sustained wind speeds in Australia, with offshore wind gusts of up to 289km/h recorded at Bedout Island before measurements stopped working.

He said the weather system might still cause flash flooding and could isolate communities and residents if roads were cut off.

Cyclone Ilsa is expected to continue moving east southeast and maintain intensity before weakening below tropical cyclone strength on Friday night as it moves into southern parts of the Northern Territory.

Communities in the NT from Yulara to Ti Tree have been asked to prepare for the possibility of gale force winds and up to 100mm of rainfall on Saturday.

"While the system will continue to weaken as it tracks east, conditions will be dangerous," NT acting assistant commissioner for the region Kylie Anderson said.

Mr Hall said authorities were focused on getting boots on the ground in towns across the region including Marble Bar and Nullagine to work out what help was needed.

Extra emergency workers, essential supplies and aircraft have been sent to the area.

Australian Associated Press