The latest case marks only the sixth instance of a child under the age of 4 testing positive for Covid-19, among 1153 confirmed cases since late February.
They included three girls aged between one and four, recorded in late March, and another boy in the same age bracket, recorded in Auckland on April 16.
New Zealand's youngest case of confirmed Covid-19 to date was a baby boy, aged under one, recorded in Waikato on April 11.
The regions which still have active cases are Waitemata, Auckland, Manukau, Waikato, Hawke's Bay, Mid-Central, Nelson Marlborough, Canterbury and Southern.
This week, New Zealand has had just five new cases of Covid-19, with three last Monday and one on Friday.
Yesterday 4211 tests were completed bringing the total number of tests conducted to 228,148 meaning 4.6 per cent of New Zealand's population has now been tested.
The country is heading into its first full week at alert level 2.
The Ministry of Health said in a statement today that as more people go back to school and work tomorrow, many will be looking forward to being around people again, but that might also make some people feel strange and anxious.
"These feelings are completely normal. It's ok to notice that it feels different and to reach out to someone to talk about it or to look for useful tips and guidance online.
"It's also a really good time to start a daily wellbeing routine that can help keep you feeling physically and mentally fit. Looking after your mental wellbeing every day helps make coping with tougher times easier."
The person was sick with symptoms in late March. They had previously tested negative but their infection only came to light after the entire school was recently re-tested.
The school said in a statement the new case didn't signal any further spread of Covid-19, "rather that the test can detect viral genetic material weeks after a person has recovered".
"Auckland Regional Public Health Service (ARPHS) confirm it is unlikely there is still virus circulating in the Marist community."
