The new case is a man in his 50s, who left Newmont's Granites Mine about 540km northwest of Alice Springs, on Friday.
He returned to Darwin, where he was infectious in the community for about 36 hours, Chief Minister Michael Gunner told reporters on Monday.
"What greatly concerns us is the potential for exposure to others," he said.
"We are facing our biggest threat since the beginning of this crisis."
It's the sixth case linked to a Victorian man who travelled to the mine via a Brisbane quarantine hotel before testing positive on Saturday.
The new case was moved to Howard Springs quarantine facility but authorities fear he may have come into contact with about 150 people while in the community.
Mr Gunner said anyone who was at the Buff Club in Darwin between 5:30 and 8pm on Friday must isolate at their home for 14 days.
The BWS bottle store in the Parap on Friday between 4pm and 4:10pm and the Darwin Bunnings store on Saturday between 10am and 10:15am have also been added to the exposure-site list, with people who visited the sites ordered to isolate.
About 400 fly-in, fly-out workers travelled in recent days to Brisbane, 250 flew to Perth and 29 headed to South Australia, with 259 remaining in the Top End.
Authorities have tested all the mineworkers who remained in the NT with 199 tests coming back negative. The remaining results are pending, Mr Gunner said.
"Our biggest concern is not the test results of these people, it's the high-risk exposure site (the Buff Club) site and close contacts of the new case," he said.
"We are still under threat and in the middle of the storm but we will come through it."
One of the positive cases travelled to NSW and is being managed by authorities there.
The most recent positive case was identified in Queensland after a woman flew via Darwin to Brisbane.
A close contact of the infected Victorian miner, who lives in Palmerston, south of Darwin, tested positive to COVID-19 on Sunday while in the Howard Springs quarantine centre.
Two miners who had not left the Tanami Desert site have also been evacuated to Howard Springs.
The lockdown encompasses the Darwin, Palmerston and Litchfield local government areas, and Wagait and Belyuen Shires, with anyone leaving their home required to wear a face mask.
Residents are only permitted to leave home for medical treatment, to obtain essential goods and services, for work considered essential, one hour of exercise a day or to provide care.