"He stayed overnight at a hotel near Wellington Airport on Saturday night, before flying on to Queenstown on Sunday morning."
Police said the man was "travelling for employment".
However, he did not have the "necessary documentation" to allow him to leave Whangārei under alert level 3.
"The man is now self-isolating in Queenstown," said the police spokesperson.
"Police are supporting the Ministry of Health to trace the man's movements in Wellington and Queenstown.
"We are also working with our partner agencies to understand how the man was permitted to fly without the appropriate documentation."
Police said queries about the man's vaccination status and Covid testing would best be directed to the Ministry of Health.
The Herald is seeking comment from that agency.
Queenstown - and the rest of the South Island - are at level 2 while the Northland regions was escalated back up to level 3 after a number of cases were confirmed in the community.