While there has been debate about what that level should be, the study team worked from a target of 50 nanomoles per litre (nmol/l) of vitamin D.
About 28 per cent of the kids fell below that mark – while 41 per cent had levels between 50 and 70nmol/l, and the rest had more than 70nmol/l.
While there were no significant differences between boys and girls, other trends emerged.
Those lacking in the vitamin were more likely to be overweight and obese, be of South Asian ethnicity, have darker skin colour or get less sun exposure.
Children classified as New Zealand European tended to have the highest levels.
And although previous studies had suggested a link between poor vitamin D levels and a lack of physical activity, in this case, the researchers didn't find any such correlation.
The researchers noted that, for most Kiwis, exposure to the sun remained the major source – yet there was no evidence regarding the safe threshold level of UV radiation exposure without increasing the risk of skin cancer.
"A balance between avoiding excessive sun exposure to prevent skin cancer, and enough sun exposure to achieve adequate vitamin D levels, is required," they wrote.
In any case, the study authors suggested supplements should be considered for high-risk children in wintertime.
"Poor vitamin D status during childhood can affect long-term health, so opportunities to intervene during childhood should be pursued."
The study comes after earlier findings, showing southern New Zealand women and their babies were at high risk of a deficiency, prompted a call for full government funding of vitamin D supplements.
That study's lead author, Dr Ben Wheeler of Otago University's Dunedin School of Medicine, said the findings raised "significant questions" about public health policies.
"This is particularly an issue in New Zealand as living further south potentially decreases one's ability to make vitamin D and the country has negligible vitamin D food fortification."
