Ports and oil production platforms have been closed, and the State Emergency Service (SES) has issued a red alert for the towns of Karratha, Dampier, Roebourne, Wickham and Point Samson, warning of a significant storm surge and local flooding.
Cyclone Clare, currently a category three storm, is expected to intensify further as it approaches the coast between Dampier and Karratha, 1,550 kilometres north of Perth, on Monday night.
SES spokeswoman Neta Gill said 1,500 people have been moved out of low-lying homes at Karratha as a precaution.
The Bureau of Meteorology said a cyclone watch is current for coastal areas from Onslow south-west to Coral Bay, and for inland parts of the Pilbara including Marble Bar and Tom Price.
Australia's two biggest ports, those at Dampier and Port Hedland, have been shut, in a move that threatens to disrupt WA's resource industries.
The ports export more than 200 million tonnes of iron ore and liquefied natural gas each year.
Dampier port harbourmaster Vic Justice said the harbour had been cleared of boats, but the port will be operational again by the end of the week.
The bureau said residents of coastal areas between Wallal and Onslow can expect gales with gusts to 120 kph, including communities at Port Hedland and Karratha.
Widespread heavy rain and flooding is also likely inland in the Pilbara region over the next few days, the bureau said.
It said winds could reach 220 kph if the system intensifies.
The Pilbara region is home to offshore oil and gas operations as well as iron ore, salt and nickel mining.