Yirrkala in East Arnhem Land will enter a three-day lockdown at 2pm on Monday after two new cases and positive waste water tests.
Galiwin'ku on Elcho Island, also in Arnhem Land, will be locked down at the same time for seven days after its outbreak grew to 19 infections.
"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 2,200-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.
An outbreak in Yuendumu and Yuelamu, about 295km northwest of Alice Springs, has also grown 13 new cases, bringing the total number of infections in the cluster to 72.
Four more residents in Alice Springs' Old Timers aged care facility tested positive, along with two in the neighbouring town camp of the same name.
There was also one new case diagnosed in nearby Alyerre Renal Hostel and six at the Alice Springs Correctional Facility bringing the prison cluster to 27 cases.
Across the NT there are 39 patients in hospital. Twenty-five have acute or severe symptoms and one is in intensive care.
There are 3951 total active cases in the NT. The majority of these are in Greater Darwin (2115), and the Alice Springs area (535).