The findings, published today in JAMA Pediatrics, also found narrow-spectrum antibiotics, recommended as first-line treatment for common childhood infections, were not associated with obesity even after multiple exposures.
Ministry of Health Chief Adviser Child and Youth Health Dr Pat Tuohy said the new study was "a useful reminder to medical practitioners to take care when prescribing broad spectrum antibiotics for children".
"In many cases a narrower spectrum antibiotic is just as effective and will often have fewer side-effects.
"At the same time, it is important to remind parents that if your GP believes that your child has a significant bacterial infection and prescribes antibiotics, you should make sure that the antibiotics are picked up from the pharmacist and that your child completes the full course as directed," he said.
Professor Wayne Cutfield of the Auckland child health research centre the Liggins Institute said it was too soon to say which antibiotics might be killing bacteria that affect the rate at which children gain fat.
"Some bacteria are more efficient at sucking out calories to give to the host [child]," he said.
"But there could be certain kinds of bacteria that are anti-obesity, so it's quite conceivable in time that there may be an antibiotic treatment that is connected to reducing obesity."
Some New Zealand experts are sceptical. Fight the Obesity Epidemic founder Dr Robyn Toomath noted that the latest study was funded by the American Beverage Foundation for a Healthy America, founded by the soft-drink industry.
"This is the industry buying crap science," she said. "People who are poor get sick and get more antibiotics. They are more likely to be fat and a lot of other things as well."
According to the latest Health Ministry New Zealand Health Survey, one in nine Kiwi children - aged 2 to 14 years - are obese and another 22 per cent are overweight.
Kiwi mother-of-two Clare Bridle said she wasn't worried about the research. Her 2-year-old son Asher has had antibiotics three times - once for a chest infection and twice for ear infections. But other times his doctor decided against antibiotics, in line with official advice to minimise the chances of developing antibiotic resistance.
Q&A
Can antibiotics make children fat?
Scientists have found that infants given antibiotics at least four times in their first two years are 16 per cent more likely to be obese by the age of 5. Other studies have had mixed results in regards to the age when it could impact on obesity.
How might antibiotics make children fat?
Scientists speculate that antibiotics may be changing children's metabolism (the way they convert food into energy) by killing some kinds of bacteria in the gut but allowing others to thrive.
Should we stop giving antibiotics to young children?
No. Liggins Institute director Dr Wayne Cutfield says it's too soon to say which kinds of antibiotics, if any, may be causing obesity. He says antibiotics should never be used too freely, but are needed to treat many childhood infections.
