Health workers are racing to find additional contacts, with a three-day lockdown in Katherine and lockout in Greater Darwin scheduled to end at midnight on Sunday.
The new case is housemate of an unvaccinated man in his 20s who was diagnosed with the virus in Katherine, 320km south of Darwin, on Thursday.
Chief Minister Michael Gunner says that man stayed at the Mantra Hotel in Darwin with a traveller from North Queensland after visiting the Monsoons pub and nightclub.
"We do know that he spent time on Friday and Saturday night with a person who had recently arrived from Cairns," he told reporters on Friday.
"So we are investigating that further and that person is now in quarantine and we are interviewing them to determine if this is the source."
Mr Gunner said the man is likely to be infected with the Delta strain and he could have been infectious in the community from Sunday until Tuesday, when he started developing symptoms.
He lives in a rural area south of Darwin and works at RAAF Tindal, near Katherine, but that site is not considered to be an exposure site.
The man moved about Darwin and Katherine before he was tested for the virus on Wednesday.
He is now quarantining at the National Centre for Resilience at Howard Springs, where he is assisting health workers with contact tracing.
Katherine was plunged into lockdown for 72 hours at 12.01am (local time) on Friday.
Greater Darwin also had health restrictions imposed, with its first lockout for unvaccinated people.
Under the new rules, only fully vaccinated people are permitted to move about the community.
Mr Gunner previously said Katherine was locked down because its 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.
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