The researchers found no differences when it came to cognitive development, but Dr Wouldes said it was still possible that disadvantages could become more apparent as the children grew older and had to meet more challenging cognitive tasks at school.
"Our early analysis of the [aged] four and a half year data suggest children exposed during pregnancy to P may find if more difficult to inhibit their behaviour and to plan and problem solve than the non-exposed children in our study."
Research among children whose mothers had used cocaine had shown the age of four and a half as a "critical" time for development, she said.
While the results suggested that development could be delayed for the exposed children, it was still unclear as to whether the effects would be life-long.
"When they get older, they may be able to catch up at developing these motor skills by playing in the playground, or learning fine motor skills in the classroom."
Until now, there had been little research on how using methamphetamine while pregnant later affected the development of children's brains.
A sister study, which tracked 330 US children aged between three and five years, earlier showed it increased the chances of children developing behavioural problems in early age.
In 2009, New Zealand had one of the highest rates of P users in the world, with 2.2 per cent of the adult population using the drug.
Although the rate of pure amphetamine use had halved since then, and the drug's street price was starting to climb, more than 25,000 New Zealanders were still estimated to be using it.
"It's a big concern, because it can be manufactured quite easily and it's a powerful drug," Dr Wouldes said.
"It makes people feel really great, until they become dependent on it."
The study:
• Researchers assessed 107 Auckland children whose mothers had used methamphetamine use while pregnant in a range of tests measuring their cognitive development and motor skill performance.
• The results showed they performed more poorly at motor skill tests, such as grasping objects.
• The researchers found no difference between children in a control group in cognitive development, but these effects were suspected to emerge in later studies testing the children at older ages.