The new study analysed data from 727 babies and their mothers who took part in the Growing Up in Singapore Towards Health Outcomes (Gusto) study.
Almost a third of the babies were born via caesarean, of which a third were elective.
Researchers compared the body mass index-for-age measures at 12 months of age in babies born by elective and emergency caesarean against babies born vaginally.
Of the babies born by elective caesarean, 24.3 percent were at risk of overweight or overweight, compared to 14.9 percent of the emergency caesarean-born babies and 13.1 percent of the vaginally born babies.
The link remained when other possible reasons for this raised risk were factored in: the mother's ethnicity, age, education, body mass index, smoking, high blood pressure, gestational diabetes.
This study was one of the first to tease out the effects of elective versus emergency caesareans.
"The most likely explanation for the difference in babies' overweight susceptibility is that babies born by elective caesarean are not exposed to their mothers' bacteria as would normally occur during labour, and nor do they undergo the stress of labour," said Gluckman, of the University of Auckland-based Liggins Institute.
Other evidence suggested these two factors – maternal bacteria and a surge in hormones such as cortisol in the baby due to the stress of labour – helped set babies on a developmental pathway to healthy weight in childhood.
"Babies born by emergency caesarean generally have already experienced some labour, and the membrane surrounding them in the womb has been ruptured, allowing mothers' bacteria in."
The researchers say that if further research bears out the link to overweight risk, health professionals should consider discussing the potential long-term effects of elective caesareans on children.
"This study waves a flag: the rising epidemic of elective caesareans – a social trend rather than a health trend – is not without some potential costs for the baby," Gluckman said.
"On the other hand, when a caesarean is indicated for medical reasons there should be absolutely no hesitation, as in those circumstances it is best for mother and baby."
The study was led by researchers from the Duke-NUS Medical School in Singapore.