Evacuated town Borroloola was spared a direct hit but experienced cyclonic winds.
A destructive and intense Cyclone Trevor has hit the Northern Territory mainland, crossing over the remote Gulf of Carpentaria coast as a category four system.
The storm, producing wind gusts of 230km/h, made landfall near the Northern Territory's border with Queensland on Saturday morning.
Evacuated town Borroloola was spared a direct hit but experienced cyclonic winds, while Groote Eylandt and Numbulwar to the north are no longer in the warning zone.
More than 2000 people had been evacuated from communities under threat from the cyclone.
It was the largest evacuation effort in the NT since Cyclone Tracy hit Darwin in 1974.
Territory authorities are now concerned about a dozen people who are believed to have remained in Trevor's path, ignoring advice to leave.
They have been urged to have supplies to last at least three days, take shelter and stay away from waterways.
The cyclone, moving southwest at 16km/h, is expected to slowly weaken to a category two system by Saturday evening.
However, its size and intensity meant Trevor would pose a danger for days.
It is forecast to produce major tidal surges and up to 200mm of rain per day, which will pose the risk of flash flooding and road closures.
"Communities and homelands in and around the Carpentaria district and extending into the Barkley district can expect the weather to continue to pick up today and into tonight," the Bureau of Meteorology's Todd Smith said.
"Now we're seeing it move inland, we'll see those gale force winds start to contract a little.
"However, the winds around the centre of the system will remain dangerous for the next 12 to 24 hours.
"It's really the next few days that's going to pose a rainfall risk to the Barkley."
Government and community organisations have been coordinating evacuation centres in Darwin and Katherine, where half the evacuees are staying.
Authorities acknowledged the situation for evacuees was difficult, while NT chief minister Michael Gunner dismissed claims on social media that Indigenous people were being afforded inferior treatment to non-Indigenous people from their communities.
"It's critical during a cyclone we do everything we can to make sure everybody is safe," Mr Michael Gunner told reporters.
"We treat everybody equally. There is some seriously bad misinformation going around right now that does nothing to help anybody."
By Sunday afternoon, forecasters believe Trevor will weaken below cyclone strength and reach Tennant Creek, 1000km south of Darwin, as a tropical low in the evening.
Residents of Groote Eylandt and Numbulwar have been told they may be able to return home on Sunday should communities be deemed safe and power and water supplies were functioning.
Trevor left behind a trail of damage in Queensland's Cape York Peninsula earlier this week, uprooting trees, causing flooding and roof damage, closing schools and roads, and knocking out power supplies.