A lack of vitamin D is also linked to a higher risk of rickets in childhood. Rickets causes soft bones, increasing the risk of fractures and deformities.
The study raised "significant questions" around public health policies, according to lead author Dr Ben Wheeler, of the Dunedin School of Medicine's Department of Women's and Children's Health.
"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."
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Vitamin D supplements are only considered for pregnant women and breastfed infants considered "at risk" - such as those with dark skin, people who avoid the sun completely, or infants who are breastfed over winter. Certain medications, liver or kidney disease and having a sibling with rickets are also risk factors.
Most Kiwi women and children don't meet these risk factors, Wheeler said.
"However, our results show that in southern New Zealand, in traditionally low risk women and their infants, rates of deficiency are very high. In addition very severe deficiency in infants was also seen, something not previously seen in other similar international studies.''
New Zealand's guidelines should be stronger, Wheeler said. He called for a fully-funded universal supplement for Kiwi women and their children during pregnancy and lactation, especially in the South Island.
Maternal vitamin D status during pregnancy is influenced by a range of factors, including season, skin colour, supplementation, latitude, and potential pregnancy-specific variations in metabolism.
Supplementation studies during pregnancy demonstrate significantly improved infant status at birth and beyond, according to the researchers.
According to the Ministry of Health, around 5 per cent of Kiwi adults are vitamin D deficient and another 27 per cent are below recommended blood levels.
Living in the South Island, particularly south of Nelson-Marlborough, is a risk factor for deficiency, as is having darker skin, covering up or not going outside often.