The man was tested, as per Northern Territory requirements after existing hotel quarantine, before driving to Katherine for work purposes.
Chief Minister Michael Gunner said it was not yet known if he was infected with the Delta strain and warned there was a very "real risk" the virus had been transmitted to others.
"We have to start by assuming the worst … we need to stop everything in its tracks so we can get on top of this," he said.
From 5pm, residents will only be able to leave home for the following reasons:
- To shop for essential goods and services
- Medical treatment, including Covid-19 testing or vaccination
- Work that is considered essential and can't be done at home
- To exercise, for no more than one hour a day, with one other person or your household.
- To provide care or support to a family member or person who cannot support themselves.
Territorians have been urged to refrain from "unnecessary movements and interactions" and to use click and collect services wherever possible.
Face coverings must be also be worn by individuals in lockdown areas.
It's the second lockdown in three months for many in the Northern Territory. Alice Springs and Greater Darwin was sent into lockdown in June after a number of workers at the Tanami mine tested positive to the virus.
Gunner made the announcement on Monday morning following an emergency meeting of the Covid-19 management team.