One explanation given by the authors was that good bacteria picked up in the birth canal by babies born by vaginal delivery may give them a distinct developmental advantage later in life.
Dr Charlotte Elder, spokeswoman for The Royal Australian and New Zealand College of Obstetricians and Gynaecologists, says this is one study to find a link and should not cause any stress.
"I'm aware of at least two others that have looked at very similar things that haven't found a link," she told AAP.
"A large number of caesarean sections are done to avoid potentially life-threatening complications, including death. So caesareans have a really important role to play, so I think saying they're aren't good is really quite dangerous."
Dr Elder acknowledges it's worth researching but the findings wont change current practice.
"This issue is a very complicated one, it's very much too simplistic to just say that having a caesarean means that your gut flora is changed therefore that means you are not going to do so well at school."
"This is just a tiny piece of the puzzle rather than being something that's worth stressing about."
Researchers at Melbourne University estimated the relationship between caesarean birth and child cognitive outcomes using data from the Longitudinal Study of Australian Children.
They tracked the development of the children every two years until age nine.
After controlling for socio-economic advantage, a "negative" relation between caesarean birth and a "range of cognitive outcomes" was found from age four to nine.
Lead author Dr Cain Polidano described the findings as small but significant and said they warranted further investigation.
Clinical psychologist Dr Liz Westrupp, a researcher at the Murdoch Children's Research Institute, says a previous study using the same birth cohort found a "mix" of positive and negative physical and mental health outcomes associated to caesarean birth.
However she said: "We didn't feel like there was really strong evidence from that data at least for strong concerns."
Dr Westrupp also noted that every child is individual and relying on NAPLAN results does not tell the full story.
Professor Ian Hickie, the co-director at the Brain and Mind Centre at the University of Sydney, told the ABC the results of the study needed to be treated with caution.
"I think there is a real danger here of this going out to the public and saying that we have shown a direct association . . . when really it jumps to some pretty interesting conclusions that this might be due to changes in the gut microbiology, that it might be related to breast feeding or not," Professor Hickie said.
"Lots of other very speculative considerations have been used in the data," he told the ABC.
"At this stage what we know is that the appropriate use of caesarean births saves lives, maternal and child."
- AAP
