Health authorities say traces of COVID-19 have been detected in wastewater samples at Darwin's Berrimah treatment plant.
However, Health Minister Natasha Fyles said no lockdown or extra COVID-19 restrictions are necessary at this stage.
The viral fragments were found in samples collected between last Friday and Tuesday of this week.
Authorities said the Berrimah catchment area covers the Winnellie and East Arm industrial areas and port, which are used by local and interstate freight and transport workers.
The Northcrest housing estate is also part of the catchment area.
In a statement, the health department said more tests of wastewater across the Darwin and Berrimah catchment areas would be undertaken.
Northern Territory's Chief Health Officer, Hugh Heggie, said all freight and transport workers should be getting weekly COVID-19 tests, in line with industry testing requirements.
"We are aware that, in other areas in Australia, freight and transport workers who are required to travel long distances have tested positive to COVID-19," he said.
"It is important that, if you have any symptoms of COVID-19, you get tested — especially if you live in Darwin or visited between September. 24 and 28"
The department said fragments could be detected when a person in the area had recovered from COVID-19 and was no longer infectious.
On Thursday afternoon, Ms Fyles said she had been briefed by health officials and no further precautions were required for now.
"It is a warning and a reminder for Territorians that coronavirus is present in the Australian community. We've seen traces today in Queensland," she said.
"Thinking it is not in the Top End community — we can't afford to have that complacency."
The announcement came hours after a code yellow was lifted at Royal Darwin Hospital, where capacity issues forced the cancellation of elective surgery for the fourth time this year.
There have been no positive COVID-19 cases in the Northern Territory since mid-August.
