The system, the size of the state of Victoria, crossed the mainland as a category four storm on Sunday morning, producing wind gusts of 230km/h around the NT's border with Queensland.
But it was expected to weaken as it tracks inland on Sunday and would be a tropical low when it reaches Tennant Creek, about 1000 kilometres south of Darwin.
That could bring up to 200mm of rain per day, according to the Bureau of Meteorology, which has issued a flood watch for the drought-hit regions and rivers around the Carpentaria coast.
"The black soils in the Barkly region have been very hard baked and so we are expecting, with those heavy falls, for rainfall to run off rather than soak in," bureau forecaster Todd Smith said on Saturday.
Earlier, the system was sustaining winds near the centre of 175km/h with wind gusts to 250km/h.
More than 2000 people were evacuated from communities in the cyclone's path as authorities urged remaining residents to prepare for flooding and "very destructive" winds.
They were warned to have supplies to last at least three days, take shelter and stay away from waterways.
It was the largest evacuation effort in the NT since Cyclone Tracy hit Darwin in 1974.
Meanwhile in Western Australia, Pilbara residents are evacuating and sandbagging homes in the path of Tropical Cyclone Veronica.
Residents in WA's far north have been urged to stay indoors in the strongest and safest part of their homes.