The news came as Australia passed the 80% double vaccination dose rate in people aged 16 and over.
The Katherine region was plunged into a snap three-day lockdown on Friday after the Territory recorded the first local case.
The first case was an unvaccinated man in his 20s who tested positive for Covid-19 on Thursday after spending time in Greater Darwin and Katherine. His housemate tested positive on Friday.
Authorities announced on Saturday that a 21-year-old woman who arrived from Cairns on the 29 October, and spent time with the man, had also tested positive. She only became symptomatic on Saturday.
Since 12.01am Friday, Katherine residents have only been allowed to leave their homes for five reasons: to access goods and services, receive medical treatment, provide care and support, perform essential work and exercise.
Greater Darwin is also locked out of Katherine in an effort to contain the spread of the virus.
The NT chief minister, Michael Gunner, said that 1,200 Covid-19 tests had been administered on Friday.
But, Gunner cautioned, it is still likely there is another undetected case out there from whom the man and woman caught the virus.
Queensland reported a new local Covid-19 case on Saturday: a woman in her 20s from Goondiwindi, a town on the border of Queensland and NSW.
Speaking outside a Bunnings store that was hosting a pop-up vaccination clinic, the Queensland health minister urged residents to get tested.
Victoria recorded 1,268 new locally acquired Covid-19 cases and seven related deaths on Saturday, bringing the total number of active cases to 16,662.
Victorian authorities confirmed that, as of Friday, there were 651 people in hospital, including 106 in intensive care. Of these, 70 were on a ventilator.
Of the cases in hospital, authorities said 84% were not fully vaccinated, while 96% of those in intensive care had not received both jabs.
In NSW, authorities reported 270 new local infections on Saturday. Three more people with Covid-19 died, none of whom were fully vaccinated.
There were 270 Covid-19 cases admitted to hospital in the state. Authorities said 55 people were in intensive care, 27 of whom required ventilation.
The ACT also recorded 18 new Covid-19 cases, bringing the total number of active cases in the territory to 136. There were only two people in ACT hospitals with the virus, one of whom was on a ventilator.
But vaccination rates vary significantly state-to-state, and are critically low in some communities.
As of Friday, the ACT was leading the way in terms of vaccinations, with almost 95% of over 16-year-olds having received both jabs.
A total of 89% of those over 16 in New South Wales, 83% in Victoria, 77% in Tasmania and 66% in Queensland were fully vaccinated.
By comparison, only 65% of residents over 16 had received two doses of a Covid-19 vaccine in Western Australia and the Northern Territory.
Analysis of the most recent data by Guardian Australia shows that the surge effort has produced some positive results, but the gap between the Indigenous and the overall vaccination rates remains high.
Overall, there is a 19 percentage point difference between the Indigenous and overall first-dose vaccination rates in most of the priority areas.
