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Unvaccinated people will be locked down until Sunday at midnight.
Chief Minister Michael Gunner said the unvaccinated man had not travelled outside the NT recently and had contracted COVID-19 locally.
"We don't know where and we don't know when but this is community transmission," he told reporters during a late night press conference.
"He has caught it from someone in the territory but we don't know who."
The man lives in a rural area south of Darwin and works at RAAF Tindal, near Katherine.
He moved about both communities while infectious before developing symptoms on Tuesday and coming forward for testing on Wednesday.
He was diagnosed with the virus late on Thursday.
Mr Gunner said it was likely the man was infectious in the community from Sunday until Tuesday but he could have been infectious from October 19.
The man is now in isolation in Katherine and will be moved to the National Centre for Resilience at Howard Springs.
There are currently five exposure sites, including Monsoons pub and nightclub in Darwin, and the RAAF base.
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Mr Gunner said people who have been at an exposure site must isolate and book a COVID-19 test.
"Right now this bloke has no idea how he caught COVID and neither do we," he said.
The chief minister also urged unvaccinated people to get the jab, saying the lockdown in Katherine had been imposed because the vaccination rate was below 80 per cent double-dosed.
Currently, 75 per cent of residents have had their first dose and 65 per cent are fully vaccinated.
The Greater Darwin lockout of unvaccinated people is the NT's first, with only double-dosed people with a vaccination certificate able to enter business and community sites.
Children are allowed to attend school and sport.
Mr Gunner said the mobile phone app for people to display their certificates is not yet ready as he urged people to be patient and polite.
"This will be clunky over the next few days," he said.
He also warned the region could go into a full lockdown if the situation deteriorated.
People in Katherine and the unvaccinated in Greater Darwin will only be permitted to leave their homes within a 5km area for five reasons.
The reasons are: medical treatment, to buy essential good and services, essential work, one hour of exercise per day, and to provide support or care to a vulnerable person.
Face masks must be worn by all people in Katherine and Greater Darwin.
NT records first ever local COVID-19 case, triggering 72-hour lockdown - SBS News
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