More than 5700 children were analysed for the study's second Vulnerability Report, made public today.
Study director associate professor Susan Morton, of the University of Auckland, said that across all risk categories 15 per cent were in the abnormal behaviour group based on the "strengths and difficulties" screening questionnaire, which is also used in the Government's Before School Check.
"They are potentially heading towards behavioural issues and problems with social behaviours."
She said the 44 per cent abnormal finding in the high-risk group was "much higher than we had anticipated".
She said the clustering and persistence of risk factors in association with potential behavioural issues asked: "How can we identify the most vulnerable children from birth and look at ways we might support them and their families, to mitigate against the effect of the developmental trajectories we are seeing even before age 2."
The questionnaire was answered for a second time at the 4-year-old checkpoint in the longitudinal study.
The study checked maternal risk factors at late pregnancy, and 9 months and 2 years old. At 2 years, 41 per cent were low risk, 46 per cent medium and 13 per cent high.
The most common risk factor was living in an area of high deprivation, experienced by at least 25 per cent of the children at the three measure points.