Carisbrook School principal Katrina Munro sent out a message yesterday saying the school had been notified by the Ministry of Health of the positive case.
The school was working to identify any close contacts of the pupil, Ms Munro said.
"The health and wellbeing of our children, staff and community is a top priority".
The school will remain open however Kakapo will move to distance learning, she said.
"If you child is in Kakapo, stay home until we provide you with an update.
There is to be an update on the situation this morning, she said.
Bradford School principal Emma Knopp yesterday said there was a "confirmed Covid-19 case in our community".
Pupils in one classroom and those who attended the before and after school care were asked to remain at home.
Balmacewen Intermediate has also been contacted over a possible case.
Principal Andrew Hunter sent out a letter this morning saying a pupil had been deemed a close contact of a positive case.
"We have been advised to take the precautionary measure of keeping one class at home today pending test results.
"I will notify you of any further developments once test results are made available."
These are just the latest schools to deal with the effects of positive cases following several others in the South this week.
Yesterday Otago Boys' High School confirmed its first case.
Rector Richard Hall said the Covid-positive person lived at the school hostel and had not been in regular contact with pupils or staff.
Current information suggested the risk to staff and pupils was minimal but the school was taking all precautions, he said.
Columba College recently spoke to pupils who had been considered casual contacts, principal Pauline Duthie said.
The pupils were tested as a precautionary measure and returned negative results.
Wakatipu High School has three confirmed Covid cases after one pupil was identified as a positive case on Wednesday and a further two suspected cases were confirmed yesterday.
Principal Steve Hall said the first case was not infectious and so did not generate any close contacts at school.
The school would be taking a cautious approach and had identified 47 close contacts of the two new cases, which included four teachers.
A Gore Main School class is also self-isolating after a pupil tested positive for Covid-19 at the weekend.
The news came after Musselburgh School in Dunedin was the first school in the South to be hit by a positive Covid case among its pupils.
Gore Main School principal Glenn Puna said three teachers, two teacher aides and about 25 pupils at the primary school were sent home on Monday.
