Tropical Cyclone Megan strikes Australia causing a mega rain bomb ...

Hundreds of isolated Aussies in the Top End have woken up to a trail of destruction after Tropical Cyclone Megan wreaked havoc overnight.

The Northern Territory town of Borroloola was in the firing line as the cyclone made landfall on the south-western side of the Gulf of Carpentaria late on Monday as a severe category 3 system.

It's been a sleepless night for the town's 700 residents who were meant to be evacuated on Monday.

But Cyclone Megan moved in faster than expected, bringing winds up to 200km/h, and heavy rain which meant RAAF aircraft were unable to land.

Instead, stranded residents were ordered to bunker down at the local police station, the town's health facility or one of dozens of dwellings capable of withstanding a category three system.

More heavy rain is expected to soak Australia's north in the next 36 hours

Residents were yet to inspect the full extent of the damage on Tuesday morning.

'It got a little bit wild and windy last night around midnight. It's still dark at the moment so can't really see too much,' Borroloola local Brad told Sunrise.

'It was quite noisy with a lot of rain.

'Once the sun comes up, we will get a look around and know the damage is.'

Megan is forecast to continue to move inland to the south-west on Tuesday before weakening to a tropical low in the morning, when it's likely to head westward.

The Bureau of Meteorology forecasts 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 on Tuesday, Northern Territory Police Superintendent Sonia Kennon said.

Residents in remote NT communities are yet to see the full extent of the damage left behind by Tropical Cyclone Megan

Heavy rain and flash flooding is forecast for parts of the Carpentaria and the northern Barkly on Tuesday morning.

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.

The wild weather forced an evacuation in Borroloola to be cancelled, leaving residents to bunker down for the night