Damaging 90km/h winds are forecast to hit the Tanami and Lasseter districts on Saturday morning before moving to western parts of the Simpson district.
Heavy rain is no longer forecast for those districts but a flood watch is still in place for the western inland region, the Bureau of Meteorology advised.
Locations that might be affected are Alice Springs, Yuendumu, Ti Tree, Papunya, Hermannsburg and southwest Tanami District near the West Australian border.
"Even though that cyclone is weakening, we are still going to see the potential impacts from the rainfall continuing over the coming days as water moves through the system," meteorologist Miriam Bradbury told ABC TV on Saturday.
"When so much rain falls in such a short space of time, it can easily lead to very rapid creek rises, as well as cutting off roads and access routes."
The severe weather is forecast to move east across the NT on Saturday, weakening as it nears Alice Springs in the afternoon.
It comes after Ex-Cyclone Ilsa caused damage to parts of remote inland Western Australia.
The system crossed the WA coast early on Friday between De Grey and Pardoo as a category five.
It was downgraded to category one by the afternoon as it tracked through the eastern Pilbara with wind gusts up to 170km/h.
Pardoo Roadhouse and Tavern, 150km northeast of Port Hedland, bore the brunt of Ilsa as it made landfall, packing record winds of 213km/h.
"We are all still a bit shaken and emotional to see the damage," they posted on Facebook.
"She may have wiped us out but she can't take away our spirit."
The owners have launched a GoFundMe page to help pay for an estimated $4 million in damage.
"The roof of our roadhouse is gone, staff rooms and buildings have been wiped out, most of the accommodation we offered onsite has been wiped out or received extensive damage," they wrote.
Telfer gold mine operator Newcrest Mining has begun assessing the Pilbara site for hazards such as fallen power lines and loose tree branches as well as any hidden structural damage.
"Pending inspections of the airstrip and village, we aim to commence bringing the majority of people back to site from tomorrow afternoon and through the remainder of the weekend," the miner said on Friday.
WA Fire and Emergency Services Commissioner Darren Klemm said the full extent of the destruction could take days to assess.
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