Yirrkala in East Arnhem Land will enter a three-day lockdown at 2pm local time on Monday after two new cases and positive wastewater tests.
The Indigenous community of about 800 people is 18km southeast of the mining town of Nhulunbuy, on the Gove Peninsula, about 700km east of Darwin.
Galiwin'ku on Elcho Island, also in Arnhem Land, will be locked down at the same time for seven days after its outbreak grew by 15 infections to 19.
"This is a very isolated part of the NT," Deputy Chief Minister Nicole Manison told reporters.
"We have many people there with complex needs."
The health restriction will apply to Elcho Island's entire 2200-strong population, including its homeland communities.
"We want to make sure we slow the spread of COVID there. That is really important (however) we think it would be very difficult to eliminate COVID-19 from Elcho," Ms Manison said.
Chief Health Officer Hugh Heggie said the lockdowns were required due to the remote locations of the communities and the difficulty moving infected people to hospital.
Meanwhile, an outbreak in Yuendumu and Yuelamu, about 295km northwest of Alice Springs, has grown by 13 new cases, bringing the total number of infections in the cluster to 72.
Four staff in Alice Springs' Old Timers aged care facility also tested positive, along with two people in the neighbouring town camp of the same name.
There was also one new infection diagnosed in nearby Alyerre Renal Hostel and six at the Alice Springs Correctional Facility, bringing the prison cluster to 27 cases.
Eighteen new cases were reported in the Alice Springs area on Sunday, mostly among the Indigenous community in camps and health and aged care facilities.
The city will remain in a seven-day lockout until next Sunday.
Across the NT there are 39 patients in hospital, 25 of whom have acute or severe symptoms with one in intensive care.
Despite the continued spread of the virus through remote NT, Dr Heggie said the number of cases on the territory was small compared to other jurisdictions.
He said the fluctuations in case numbers in the past week that led to the daily figures rising and falling between 284 and 594 infections was probably linked to self-reported RATs and New Years Eve celebrations.
There are 3951 active cases in the NT. The majority of these are in Greater Darwin (2115), and the Alice Springs area (535). The remainder were in regional areas.
About 30 per cent of the territory's 246,500-strong population are Indigenous.
The NT detected 327 new case on Sunday, 412 on Saturday, 546 on Friday, 550 on Thursday, 352 on Wednesday and 594 on Tuesday.
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