The Bureau of Meteorology confirmed Tropical Cyclone Narelle touched down at 7am Queensland time on Friday while Lockhart River, Coen, and Port Stewart residents have been warned to take immediate shelter.
Wind speeds near the centre of the cyclone have hit 195km/h, with wind gusts reaching 270km/h.
Cyclone Narelle is now moving westward and is crossing the area between Lockhart River and Coen.
Senior meteorologist Sarah Scully warned the system would cause large airborne debris, major structural damage, and property destruction.
"Satellite data is indicating that there's widespread winds near the centre of the system, well in excess of 200 km/h," she said.
"Very destructive winds may start to be experienced within the next hour ahead of the coastal crossing. Winds of this strength have the potential to cause significant structural damage to buildings and property, such as significant loss of roofs."
Emergency alerts have been issued urging residents in the remote communities of Lockhart River, Coen, and Port Stewart to take immediate shelter.
"Take shelter now in the strongest part of the building you are in," the warning said.
Narelle was on course to be the first category five system to hit Cape York since Cyclone Mahina killed more than 300 people in March 1899. It was downgraded to category 4 on Friday morning.
— Wing Kuang, AAP