The Greater Darwin lockdown ended at midday (local time) on Thursday as planned but Katherine, 300 km south, will remain under wraps until Friday.
"We need Katherine to hang tight for another day," Chief Minister Michael Gunner told reporters on Thursday.
Mr Gunner said the man was more infectious while he was in Katherine and the town of 8000 is a busy hub with links to many remote Aboriginal communities.
Contact tracers are also yet to find 12 people who potentially crossed paths with the man at the local Woolworths.
"I am sorry you have to do this for another 24 hours, this is the recommendation of our health experts," Mr Gunner said.
Authorities still don't know how and where the man contracted the virus.
The infection has been confirmed as a strain of the Delta variant but it hasn't yet been linked to any other cases in the country.
"The source of this infection remains a mystery," Mr Gunner said.
"It is probably one of the most unusual cases we have seen in Australia."
Some restrictions will remain in place in the lockdown areas for seven days. These include wearing face masks in public when people can't socially distance themselves.
Patrons will need to be seated at hospitality venues and gyms and markets will remain closed for a further week. People can have a maximum of 10 visitors to their homes
Schools will reopen on Friday and Darwin Festival events can resume.
The infected man in his 30s arrived at Darwin Airport on a Qantas flight just before midnight last Thursday and travelled to the Hilton Hotel by taxi.
He returned a positive result on Sunday night after mandatory testing at Royal Darwin Hospital earlier in the day.
Before the results arrived, he drove to Katherine for work, where he met a friend at a resort and visited Woolworths.
He previously returned a negative COVID-19 test on August 10 during his 14-day stay in a Sydney quarantine hotel.