Chief Minister Michael Gunner says the outbreak represents the Northern Territory's biggest crisis since the beginning of the pandemic.

The lockdown started at 1pm Sunday after 900 workers left Newmont's Granites Mine about 540km northwest of Alice Springs, where a Victorian man had earlier tested positive.

About 400 fly-in-fly-out workers travelled in recent days to Brisbane and 250 flew to Perth, with 244 remaining in the NT.

NT authorities moved fast to track down those people who stayed but they were unable to find about 20 by Sunday morning.

It prompted Mr Gunner to order the Top End into lockdown.

There was a need to "assume the worst, assume they are positive and assume that there are exposure sites".

The 20 people have since been found and ordered to isolate but more cases are likely.

"Everything we see points to this being the highly-infectious Delta variant," Mr Gunner said.

"We are expecting more cases.

"There is a stronger chance that any new cases will have exposure sites which makes the job of tracing and testing much bigger."

Mr Gunner said one of the five positive cases had travelled to NSW. Another positive case has been identified in Queensland.

Two from the cohort are isolating at the mine in the Tanami Desert but would be evacuated to the Territory's Centre for National Resilience at Howard Springs.

The fifth case was a close contact of one of the mine workers, who lives in Palmerston south of Darwin. He tested positive to COVID-19 while in the Howard Springs centre.

Mr Gunner said the Palmerston case involved a 64-year-old employee of the mine who had travel by plane to Darwin on Friday.

He was picked up by his wife and went straight home to Palmerston.

His only other travel was to collect his adult daughter from her workplace and he did not leave the car. His wife and daughter had no additional movements.

When interviewed on Saturday, the man told contact tracers he was isolating at home with his wife and daughter and had developed symptoms.

From there, he was immediately tested and taken to the Centre for National Resilience.

Darwin, Palmerston and Litchfield local government areas - and the Wagait and Belyuen shires - entered a 48-hour lockdown 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.

Australian Associated Press