Southern District Health Board Medical Officer of Health Dr Michael Butchard said the person was interviewed by Public Health South after arriving in Dunedin and the public health risk was assessed as low.
Out of an abundance of caution, the person was asked to get a Covid-19 swab, which was negative, Dr Butchard said.
Public Health South asked that the person "take their alert level 4 with them" - act as if they were in level 4 lockdown conditions despite the South Island moving down to alert level 3 from 11:59pm.
The person was currently doing this, Dr Butchard said.
A Civil Aviation Authority spokesman referred comment to police.
Inquiries in relation to whether enforcement action would be taken were ongoing, police said.
Stuff is reporting the student was female and two of her flatmates raised concerns after they heard another flatmate was going to pick her up from Dunedin Airport.
The two flatmates were now staying in a university-owned property, while the returning student was told to self-isolate at a Castle St flat, Stuff said.
A University of Otago spokeswoman said it was working closely with police and the Ministry of Health on the matter and could not comment on the particular situation given a police investigation was under way.
"We are doing all we can to support the impacted flatmates and we have ensured they are not residing at the same address," she said.
"All students, along with all other New Zealanders, need to obey the Government's Alert Level guidelines.
"We have been impressed with how, overall, students have complied with the Government's rules. With the mid-semester break under way this week, many students were looking forward to returning to their homes.
"We very much appreciate our students' co-operation and understanding of how important the Government rules are."
The university was regularly communicating with students and would advise when Government rules allowed students to return south to study, she said.
