Tropical Cyclone Trevor has been downgraded to a tropical low, but will continue to bring heavy rain as it weakens further and reaches outback communities on Sunday.
The weather system, which was almost the size of New South Wales, made landfall as a category four storm about 100 kilometres to the south-east of Port McArthur at about 11:00am on Saturday morning.
By Saturday night it was making its way inland and had been downgraded to a category one system, the Bureau of Meteorology said.
The system is expected to weaken further as it moves into the Barkly District, and will likely fall below cyclone strength on Sunday morning while west of Brunette Downs.
It is then expected to turn into a rain depression, Bureau of Meteorology NT manager Todd Smith said, bringing 100 to 200mm of rain per day through the outback Barkly region and to communities near the Queensland-NT border on Monday and Tuesday.
Residents in those areas have been urged to ensure their emergency plans are in place and their emergency kits include several days worth of water.
The heavy rainfall may continue until Wednesday, when a high pressure system is expected to push through and clear the system out.
The communities of Ngukurr and Numbulwar saw 50 to 100mm on Saturday, while Nhulunbuy received 120mm on Friday night.
Residents set to be affected by the storm system have been advised to beware of flash flooding.
Mr Smith warned some parts had received hardly any rain in the past nine months, so in the coming days rainfall was more likely to run off the baked ground than soak into it.
Winds to remain dangerous for another 24 hours
Mr Smith said because the system was so large, gale force winds were being felt 250 kilometres from its centre.
Mornington Island, which is 200km from the storm, recorded gusts of 105 kilometres per hour and received a 1.5m storm surge on Saturday.
"So that's sort of category one wind strength," Mr Smith said.
"Now that we're seeing it moving inland we'll see those gale force winds start to contract a little, however the winds around the centre of the system, around that core, will remain dangerous for the next 12 to 24 hours."
He said the town of Robinson River would have sustained significant damage.
"Robinson River certainly, it's further to the east of Borroloola so [the cyclone is] passing very close to that," Mr Smith said.
"So I would imagine there would be some significant damage to infrastructure and vegetation through that part of the world."
The cyclone is forecast to track between Elliot and Creswell Downs and Brunette Downs during the early hours of Sunday morning.
Residents in coastal communities to the east were asked to be wary of a severe storm surge.
Residents around Tennant Creek were encouraged to prepare their homes and businesses ahead of any possible rainfall and strong winds caused by the cyclone.
The Roper Highway, Carpentaria and Tablelands Highways remained closed.
Territorians evacuate ahead of monster storm
Around 2,100 evacuees registered with the NT Government at shelters in Katherine, Tennant Creek, Darwin and Nhulunbuy.
Many others who self-evacuated were not included in this figure.
By Saturday evening a number of small outstations had been evacuated in the Barkly region, with residents moved to a 130-bed shelter at the Tennant Creek High School.
It is believed four people refused to be evacuated from remote Vanderlin Island, while at least two stayed in Borroloola.
Another two are believed to be at a wildlife sanctuary near the Queensland border.
At McArthur River mine, about 100 kilometres from the coast and to the west of the cyclone forecast track, staff spent Saturday preparing and a bunker is now set up ready to house more than 60 people.
NT regional emergency controller Travis Wurst said even though warnings had now been lifted in some communities, his crews were still assessing whether it was safe for evacuated residents to return.
He said Angurugu and Umbakumba residents had been cleared to start returning home from Sunday morning, although he encouraged the evacuees to stay in their registered shelters on Saturday night and prepare to travel at first light.
Numbulwar residents in Katherine will begin travelling home by bus from Monday.
Safety teams will begin inspecting the Borroloola and Robinson River areas from Sunday morning.
Mr Wurst said people who had evacuated Bickerton Island were not yet cleared to return home, but the matter would be assessed on Sunday.
"We have people surveying those communities and the connecting roads that were affected by severe Tropical Cyclone Trevor," Mr Wurst said.
"One of the things that we're concerned about is preserving vital infrastructure for these remote areas and restoring telecommunications, power and water to communities that have had their supplies affected."
Disaster assistance will be made available for Borroloola, Groote Eylandt and Numbulwar residents who are affected by the severe weather and flooding brought on by Tropical Cyclone Trevor.
This will be provided through the Territory and Federal governments to cover clean-up costs and help them with their immediate needs after returning home.
Further information about the assistance can be found at SecureNT.