Cyclone Rusty has weakened to a category two system as it moves inland towards Marble Bar in Western Australia's Pilbara.

Port Hedland was expected to bear the brunt as the system crossed the coast yesterday afternoon as a category three storm, but only minor damage has been reported there at this stage.

Communities between Pardoo and Nullagine are now on red alert and people there are being told to stay indoors, while towns between Nullagine and Newman have been told to prepare for cyclonic weather.

The system is still expected to pack winds of more than 165 kilometres per hour at its core and is tipped to dump up to 600 millimetres on the Pilbara.

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Department of Fire and Emergency Services spokesman John Franklin says Marble Bar residents need to be prepared.

"We're anticipating probably higher rainfalls, so that's of concern and winds that could be gusting so people have to be on alert and be aware of their surroundings and what they need to be thinking about doing," he said.

An all clear has been issued for Port and South Hedland. Mr Franklin says little damage has been reported there.

"We probably had something in the order of seven to 10 calls ... of minor damage," he said.

"It might have been a caravan that was unstable due to some winds, the roof sheeting may be dislodged, nothing major, and no reports of rooves that had been ripped off or anything of that nature."

South Hedland police Senior Sergeant Ron Patchett said the towns appeared to have sustained only minor damage.

"We were expecting the worst, we were expecting to get smashed," he said.

"As much damage as going to be possible that a cyclone could do was going to be experienced here, and as a result we're all feeling a bit lucky.

"[It was] category one near Newman late (Thursday) evening but that could quite easily drop to a low."

The cyclone crossed the coast near Pardoo, where there is a cattle station and a roadhouse.

Ian Badger at Pardoo Roadhouse said the winds were strong and the rain steady.

"It's just a matter of hanging on. The amount of water that's around is a bit worrying," he said.

"The ground is very sodden, very soft. As soon as you get a get a bit of strong wind, trees start going over."