Some 700 residents in the town of Borroloola faced the worst of the cyclone, which made landfall on the southwestern side of the Gulf of Carpentaria late on Monday as a category 1 storm.
The community was due to evacuated ahead of the cyclone but RAAF aircraft were unable to land due to the severe conditions.
Residents were instead told to shelter at the police station, health facility or dozens of dwellings capable of withstanding a category three system.
Megan is forecast to continue to move inland to the southwest on Tuesday before weakening to a tropical low in the morning, when it's likely to head westward.
The Bureau of Meteorology forecast the town would cop maximum wind gusts of up to 130km/h and a 24-hour rainfall total of more than 200mm.
An evacuation of the McArthur River Mine was also called off due to the conditions.
Defence force personnel remain on standby to assist with recovery from Tuesday, Northern Territory Police Superintendent Sonia Kennon told reporters.
Heavy rain and flash flooding is forecast for parts of the Carpentaria and the northern Barkly are on Tuesday morning.Â
Six-hourly rainfall totals between 80 to 150mm are likely, with a 24-hourly rainfall total of up to 200mm and wind gusts of more than 90km/hr.
The cyclone warning zone stretches hundreds of kilometres along the coast of the Gulf of Carpentaria.
Almost 600mm of rain fell at Groote Eylandt over the weekend as the severe weather system moved over the remote island communities.
The wharf on the GEMCO manganese mine was damaged by one of its ships carrying manganese and fuel.
NT police said there was no leakage and authorities were working to remove the ship from the wharf.
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