Authorities are warning of the potential for flooding across parts of the Northern Territory in the coming days as the remnants of ex-Tropical Cyclone Ellie move inland. 

The category-one storm made landfall overnight on the north-western coast of the Northern Territory after intensifying in the Timor Sea, bringing wind gusts of up to 110 kilometres per hour.

Speaking this morning, Chief Minister Natasha Fyles said there had been no reports of significant damage to the communities of Wadeye and Peppimenarti, close to where the storm made landfall.

At 10:30am, the Bureau of Meteorology (BOM) downgraded the system to a tropical low as it moved inland. 

The BOM warned there was still the possibility of wind gusts up to 90kph near the system, as well as heavy rainfall leading to flash flooding.

Ms Fyles urged territorians to heed the warnings of emergency services and reconsider the need for any non-essential travel through parts of Central Australia.

She said forecasters were expecting a "significant amount of rainfall" in areas on the western side of the Northern Territory, leading to the possibility of flooded roads.

"The Bureau of Meteorology is looking at 200 to 300mm of rain over the coming days [in the Tanami region]," she said.

The BOM this morning issued a severe weather warning for much of the north-western corner of the Northern Territory, including Greater Darwin, Katherine, parts of Arnhem Land and the Daly and Gregory region, for heavy rainfall and damaging winds.

Acting NT Police Commissioner and territory controller Murray Smallpage said while the storm was now moving inland, it was still dangerous.

"The future looks to be significant rainfall and potential flooding as the cyclone and subsequent tropical low moves south through into Central Australia," he said.

Acting Commissioner Smallpage urged people to take care, particularly on the territory's roads. 

"The last thing a Northern Territory police officer wants to be doing is knocking on someone's door with some tragic news about a road death," he said.

He said communities in central Australia were "well prepared" for the wet weather and a emergency operations centre had been established in Katherine to manage the remnants of Tropical Cyclone Ellie.

Deputy director of Northern Territory Emergency Services Robert Evans said there was concern that the rain moving south could impact the Stuart Highway next week. 

"But that will be depend on the rain that falls as a part of that cell as it moves through," he said. 

BOM senior forecaster Sally Cutter said although the rain would ease off in the Top End as the ex-cyclone moved south, there would be more falls next week. 

'No significant' damage from storm

Wadeye, which was one of the communities threatened by ex-Tropical Cyclone Ellie as it tracked towards the NT coast overnight, has been the scene of unrest over the last year which has resulted in more than 100 homes being destroyed.

But Ms Fyles said government agencies had "done a lot of work" to house residents in recent months and the local school was on stand-by to become a cyclone shelter if needed. 

Acting Commissioner Smallpage said the storm was "not as severe as people anticipated" in Wadeye, saying "everyone had shelter" in the community to ride out the storm.

"I spoke to the local emergency controller ... and there was adequate shelter for everybody in affected areas," he said.

Peppimenarti resident Chris Kassman said winds and rains peaked for more than three hours overnight, and he could "hear trees breaking" as Ellie passed through.

He said trees and fences were damaged but there was no significant damage to homes.

"We're all good with the electricity," he said.

"There's still a bit of work to do today, just to clean up the roads and try and help residents cut up the trees."