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Dr Sheila Skeaff led a study which tested the iodine levels of 147 children aged 8-10 at randomly selected schools in Dunedin and Wellington.
They found the median level of a short-term marker called urinary iodine concentration (UIC) was almost double the level found in a 2002 study, before the use of iodised salt in bread was made mandatory in 2009.
However, the median level of a long-term marker called protein thyroglobulin (Tg) in the children's blood showed there was still a "mild iodine deficiency" among New Zealand children.
The raised Tg levels suggested some New Zealand children might still have enlarged thyroids because they were not getting enough iodine and showed there was still "room for improvement".
Dr Skeaff said iodine was an "essential nutrient" and important for the development of the brain.
This was shown in a 2009 study in which Dr Skeaff and colleagues revealed correcting mild iodine deficiency led to "small but significant" improvements in children's performance in cognitive tests.
The latest study showed fortification of bread had been a "success", as before 2009 New Zealand had "pretty low iodine status" compared with other developed countries, Dr Skeaff said.
However, the results were still low enough to suggest fortifying other staple foods, such as pasta or cereals, should be considered, she said.
"There are a lot of people who don't eat bread or who eat very little bread and ...they will still be exactly where they [were] in 2009," she said.
Steps parents could take to increase their children's iodine intake included using iodised salt or feeding them foods such as eggs, fish and dairy products, which were good sources of iodine.
Recent changes in dietary habits, which included people eating more processed foods and staying away from salt to reduce blood pressure, had caused a re-emergence of iodine deficiency in some countries, she said.