Vaccine uptake is lagging in 33 of the 51 communities that report results to the NT government.
Some, like Alpurrurulam 1206 km southeast of Darwin, have first-dose rates below 10 per cent.
It may see the communities fail to reach the required 80 per cent fully vaccinated rate in November.
That's when the NT plans to introduce sweeping stage three changes to its COVID-19 management plan, including new border, quarantine and lockdown rules.
It won't automatically mean the COVID Delta strain will make its way to the NT from Sydney and Melbourne, but it will relax quarantine requirements for vaccinated travellers.
The Northern Land Council has urged Chief Minister Michael Gunner not to "throw Aboriginal Territorians under the national plan bus".
"Do not abandon us or expose our communities to a very real threat that we know will - literally - tear our communities apart," chairman Samuel Bush-Blanasi said on Wednesday.
"The NLC recommends the NT government adopt the very cautious and sensible approach."
Vaccine hesitancy linked to misinformation about its safety has been blamed for the slow uptake in the Barkly region and Central Australia.
The NT government says it's watching vaccination rates in remote communities and further health restrictions could be imposed in low vaccination areas to protect vulnerable residents.
The NLC's plea comes two days after Health Minister Natasha Fyles said she was extremely concerned about the low vaccine uptake.
"Some communities, where it might be just a couple of hundred people, we have virtually no protection with the vaccine," she said.
"We have visited those communities multiple times, we have provided information in language (and) we are working with community leaders."
Ms Fyles also said she expects the Delta strain to arrive in the NT "at some point".