Tropical Cyclone Rusty has intensified and is expected to unleash a significant storm surge in northern Western Australia.

Authorities are warning residents in low lying areas to evacuate with a threat of flooding, high winds and a coastal tide.

People in low lying areas of Port Hedland including a small section of Pretty Pool should relocate now, states an emergency relocation order, issued on Tuesday morning by the Department of Fire and Emergency Services (DFES).

"Rapid and powerful flooding is very likely as Severe Tropical Cyclone Rusty crosses the coast."

The Bureau of Meteorology says the cyclone has increased to a Category 3 overnight and, at 5am (WST), was estimated to be 170 kilometres north-northeast of Port Hedland and 320 kilometres northeast of Karratha.

The cyclone is moving at eight kilometres per hour towards the coast.

The relocation order urges residents to turn off the electricity in their homes, lock all doors and windows, and make sure neighbours are aware of the emerging threat.

A refuge has been set up at Port Hedland's Andrew McLaughlin Community Centre.

Destructive winds are forecast to reach up to 195km/h between Port Hedland and Wallal on Tuesday.

Gales are already occurring between Sandfire Roadhouse and Whim Creek and may extend further west to Karratha later in the day.

But the slow speed of the cyclone has made it difficult to forecast when it will finally make landfall, the weather bureau says.

Very heavy rainfall is expected to lead to major flooding in the De Grey catchment area.

More than 830mm of rain has so far been dumped on the Cocos Islands in the past few days - eclipsing the amount that fell in metropolitan Perth in 2012 by more than 200mm.

Bureau spokesman Neil Bennett says Rusty's intensity, size and slow movement is also likely to lead to a dangerous storm tide, including damaging waves.

Mining giant Rio Tinto says it has prepared for the storm by closing its Cape Lambert port facilities and is finishing up ship-loading at its Dampier ports.

The Port Hedland Port Authority evacuated the port on Sunday night and said it would stay closed.

Virgin cancelled flights from Perth to Broome on Monday, and local businesses reported a dash to buy water and tinned food as the storm approached.