The student is the son of a Dunedin man who contracted COVID-19 after returning from Europe.

He developed symptoms after he returned to New Zealand. Later on, two of his family members were also showing symptoms. All three people are currently in self-isolation.

The school's co-principals, Kristan Mouat and Peter Hills, told parents about the positive diagnosis in a letter on Tuesday, Stuff reports.

The Ministry of Health said in a statement that the school is working with education staff and health officials.

"The school is to close for 48 hours while close contacts are traced and put in self isolation and is monitored by health officials daily. Other contacts will be given advice about what to do if they become unwell. The school will be carefully cleaned before reopening," it says.

The school will not reopen until it is cleared to do so by health officials.

"The Ministries of Education and Health are working closely with public health services in Dunedin and the school to help minimise disruption, progress contact tracing and reduce the possibility of spread," the statement says.

The Ministry of Health's Director-General Dr Ashley Bloomfield said earlier on Tuesday that since the man, who is in his 40s, showed symptoms five days after returning to New Zealand, there is no need for contact tracing for people who were on his flight.