Chief Minister Michael Gunner made the announcement at a late night press conference on Thursday night.

Mr Gunner said an unvaccinated man in his 20's who works as a contractor at the RAAF Base Tindal near Katherine returned a "strong positive" result on Thursday evening after developing symptoms on Tuesday.

He said this was the first case of community transmission in the NT as the positive case has not recently travelled outside the Territory.

"We don't know where, we don't know when, but this is community transmission," Mr Gunner said.

The Katherine LGA will go into a full lockdown until midnight Sunday as authorities are not aware of where the man contracted the virus and because the Katherine region has not reached 80 per cent vaccination.

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The Tindal RAAF Base is now an exposure site as the man worked while infectious on both November 1 and 2.

The Katherine Club is also an exposure site, with anyone who was there between 5pm and 6pm on November 1 required to isolate and get tested.

The man also spent time in Darwin, with Darwin going into a 72-hour "lockout" from midnight meaning fully vaccinated people in greater Darwin will be able to move freely in the community while wearing a mask.

Unvaccinated people in Darwin will be forced into lockdown conditions.

Acting Chief Health Officer Dr Charles Pain urged people to come forward to get vaccinated, with vaccination being one of the reasons people are allowed to leave their house during lockdown.

"We do need our community to help with this. We do really need people to come forward and get tested...and get vaccinated.

"It's absolutely perplexing that people still think they should delay that decision."