"Boys, particularly Maori boys, who were exposed [to P] are lagging behind girls in motor skills and cognitive development just before formal school entry," study co-author Dr Trecia Wouldes, a senior lecturer in the Department of Psychological Medicine at Auckland University, told the Herald on Sunday.
"This can lead to conduct issues such as an inability to sit still or being able to manage their own behaviour properly.
"The problem may get magnified as the boys go through school and they could be labelled as problem kids.
"This can be remedied but they will require extra attention and will perhaps need to learn in a different way from other children."
As well as the effects on motor skills and cognitive development, children most affected by their mother's P use also didn't perform as well at physical activities and sports.
"They are not running as fluidly or balancing as well," Wouldes said. "It is doubtful if any future All Blacks will emerge from this group."
Wouldes added new research indicated alcohol could also play a part as many of the mothers who used P were also heavy drinkers.
Katrina Casey, the Ministry of Education's head of sector enablement and support, said the ministry was working closely with schools to help identify and support children who may need extra help.
"For some of these children, that may be down to the impact of their mother using drugs during pregnancy," Casey said.
"Teachers may become aware of possible maternal drug or alcohol-related impacts on a child when trying to understand the reasons for their behaviour."
Until now, there had been little research on how using methamphetamine while pregnant later affected the development of children's brains.
A spokesman for the Ministry of Health said the meth and pregnancy project would be useful for gauging the scale of the issue.
"The study will be of interest to the ministry when it is completed as it is casting some light on a problem that has not previously been quantified."
The spokesman added the ministry does not have any figures as to the health and wider social costs - but the research study may also help with this.