Residents of Katherine partially emerged from lockdown at 3pm on Sunday, joining Darwin in a 'lockout' where only vaccinated people can move about in the community.
Both Katherine and Darwin will then remain in a lockout situation until midnight on Monday.
It comes as the Northern Territory reported no new cases of COVID-19 on Sunday, and it was revealed the source of the current outbreak was a 21-year-old woman who tested positive on Saturday and lied on her border declaration form.
Five hours of interviews revealed the woman who arrived in Darwin from Queensland on 29 October had spent four days in Victoria last month, including some time in Melbourne "where she almost certainly contracted the virus", Chief Minister Michael Gunner said.
She then drove back to Adelaide before flying to Cairns and then onto Darwin.
The woman spent last weekend with the man at the Mantra Hotel in Darwin. The man then tested positive to the virus on Thursday in Katherine, 320km south of Darwin, where he works at RAAF Tindal. He was originally thought to be the index case.
The 21-year-old woman has been issued a $5,024 fine will also pay for her time in Howard Springs quarantine.
“These actions have put the Territory at risk,” Mr Gunner said.
“They forced Katherine into lockdown and forced Katherine businesses to shut. While there were compassionate reasons for her decision to visit Victoria, there were not compassionate reasons to lie entering the Territory from a hotspot.”
Mr Gunner said the discovery of the source of the cluster was “very good news” and meant the Territory remained “community transmission free”.
"We've had a doughnut day, no positives and we now know the source of the infection. I'm confident that come midnight tomorrow, we can transition out of the lockout. So keep doing what you are doing, you are doing great," he said.
The decision to extend the Greater Darwin lockout by 24 hours was to allow authorities to get on top of contact tracing and testing, he added.
He listed a number of on Sunday, a full list of which can be found on the .
Mr Gunner said there were 123 close contacts in the Territory and 119 isolating.
The Chief Minister also commented on a protest against the lockout in Darwin on Saturday where demonstrators lashed out at police officers.
"The behaviour that we witnessed yesterday where people chose to confront and throw objects at our police during a lockout, when police resources are heavily tasked, was completely un-Territorian," he said.
"I thank our police heroes for their professionalism and restraint. There were difficult circumstances. You have my 100 per cent support. I also think the overwhelming majority of Territorians doing the right thing, staying safe and getting vaccinated."
Eighty-nine per cent of people 16 and above have received their first dose of a COVID-19 vaccine while 76 per cent are fully vaccinated.
Fifty-six per cent of 12 to 15-year-olds have now received a first vaccine dose, while 33 per cent are fully vaccinated.
