The cluster in Galiwin'ku on Elcho Island, 515km east of Darwin, has grown to 87 cases, with many residents unwilling to leave their overcrowded homes and travel to the Centre for National Resilience quarantine facility near Darwin.
"For the first time we are bringing in AUSMAT to help us at Galiwin'ku," Health Minister Natasha Fyles told reporters on Monday.
"This is really important. It provides additional resources."
Ms Fyles said the health team was working to evacuate more infected people from the island in Arnhem Land, with the most severely ill transferred first.
The Australian Defence Force will help transfer people from Alice Springs and Galiwin'ku to the Darwin quarantine facility, which has a capacity of about 2000.
There are currently 600 people isolating at the Centre for National Resilience and Alice Springs quarantine facility with many more expected as the outbreak among the territory's Indigenous population grows.
Nine new cases were found in an Alice Springs town camp and at the local prison.
"We have put extra resources into the prison. The total there is 89 (cases)," Ms Fyles said.
There were also 12 new infections at the Barkly low-security prison work camp, as the outbreak there grows to 66 cases.
Ten new infections were detected at Yuendumu, 295km northwest of Alice Springs, and two cases at nearby Yuelamu.
Two new cases were reported at Amoonguna and one at Ntaria, also known as Hermannsburg, bringing the outbreak there to 35 infections.
The Utopia cluster, 240km north of Alice Springs, also continues to grow with one new infection bringing the cluster to 30 infections.
"But we have seen weather impacting access for testing," Ms Fyles said.
The community of about 1000 remains locked down and vaccination rates remain stubbornly low at 42 per cent double dosed.
Seven new cases were reported in the Pine Creek area, 220km south of Darwin, as the cluster grows to 11.
The virus is continuing to spread in other Arnhem communities with 19 new infections diagnosed in locked down Gunyaŋara, also known as Ski Beach, bringing that outbreak to 24 cases.
Infections were also detected in Yirrkala, Nhulunbuy and Alyangula, on Groote Eylandt in the Gulf of Carpentaria.
Authorities are also concerned about the Tiwi Islands with 16 new cases diagnosed in two communities.
Meanwhile, 115 people have been moved from Mission Australia's Darwin homeless shelter to the quarantine facility after 35 infections were detected.
There are now 78 infected people in territory hospitals with eight requiring oxygen and four in intensive care. About half of these are unvaccinated.
Of those, 31 are in the Alice Springs hospital, two are in Katherine, seven are in Tennant Creek, one Nhulunbuy and 38 in Royal Darwin Hospital.
Acting deputy chief medical officer Marco Briceno said many infected patients were in hospital for existing medical conditions.
"We are seeing COVID affecting more Indigenous Territorians, affecting people in high-risk settings and those individuals tend to have a higher need for hospital care," he said.
Across the NT, there are about 3900 active cases with the seven-day rolling average falling under 400 infections per day for the first time in weeks.
"We are seeing bumpy results in our testing because of the isolated conditions we live in in," Ms Fyles said in reference to the many remote communities dotted across the territory.
About 30 per cent of the territory's 246,500-strong population are Indigenous.
The NT detected 212 cases on Sunday, 314 on Saturday, 432 on Friday, 459 on Thursday, 418 on Wednesday, 625 on Tuesday, and 284 on Monday.
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