But experts have urged caution about interpreting the study's results, saying it could be that children at higher risk of developing allergies are simply breastfed for a longer time.
The study investigated the link between breastfeeding and nut allergies in 15,000 children in the ACT.
It found the risk of developing a nut allergy was one-and-a-half times higher in children who were only breastfed in their first six months.
But children fed food and fluids other than breast milk were more likely to be protected against nut allergies, the Australian National University study found.
ANU Medical School's Professor Marjan Kljakovic said although the study did not examine maternal diets, it was more likely the eating habits of mothers rather than the breast milk that was the problem.
"I think people should discourage the eating of nuts during pregnancy and breastfeeding," Prof Kljakovic told AAP.
However, Murdoch Children's Research Institute (MCRI) researcher Jennifer Koplin disagreed.
She said women were currently not advised to avoid nuts during pregnancy or breastfeeding.
"There's absolutely no strong evidence that eating nuts while pregnant or breastfeeding will cause allergy," Ms Koplin told AAP.
She said previous studies by MCRI had shown that children at risk of developing allergies were often breastfed for a longer term.
For example, if a child showed signs of eczema the mother would be more likely to breastfeed longer in the belief it could help, she said.
MCRI researchers have conducted studies showing that the timing of introducing children to foods such as milk, eggs and nuts could be crucial in reducing the risk of developing allergies.
Of more than 15,000 children surveyed at all of the ACT's primary schools, five per cent who had only been exposed to breast milk in the first six months had a nut allergy.
Meanwhile, 3.7 per cent who had breast milk and other fluids had a nut allergy, and only 2.7 per cent of those who were not breastfed at all were allergic to nuts.
"Our results contribute to the argument that breastfeeding alone does not appear to be protective against nut allergy in children," said Prof Kljakovic.
"It may, in fact, be causative of allergy."
The research was published in the International Journal of Pediatrics.