The Bureau of Meteorology confirmed Ilsa reached the coast near Pardoo Roadhouse, about 100km from Port Hedland, just after midnight (2am AEST).
BoM senior meteorologist Dean Narramore told the ABC that the system was tracking inland towards Marble Bar on Friday morning.
Sky News Australia meteorologist Bradlyn Oakes said severe weather conditions are expected to continue in WA as the system heads into southern parts of the Northern Territory.
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