It is the first case of the new variant detected in the territory.

The man in his 30s arrived in Darwin on a repatriation flight from South Africa on Thursday and his positive virus result was confirmed on Friday evening.

It comes as two more residents from Binjari Aboriginal community were diagnosed with the virus.

"It's not unexpected," Health Minister Natasha Fyles said on Monday of the ongoing infections in the community.

A 17-year-old girl who was a household contact of another case was in the Howard Springs facility when she was diagnosed.

A 19-year-old woman became infected while locked down at the community, about 330km south of Darwin.

It brings the current outbreak to 58 cases.

Meanwhile, the first round of tests in the remote community of Lajamanu, 900km south of Darwin, have come back negative.

More test results are due late on Monday.

"Everything is looking positive but it's certainly early days," Ms Fyles said.

The community of about 1000 was put into lockdown on Saturday after the virus was detected in wastewater sampling.

Lajamanu has a low vaccination rate, with only about 35 per cent of residents double-dosed.

Ms Fyles said 20 doses had been administered since Saturday.

Lajamanu remains locked down.

Binjari is in a hard lockdown, with residents only permitted to leave their homes in an emergency or for medical treatment.

Greater Katherine, 320km south of Darwin, is under a lockout.

Australian Associated Press