Those who were in the overweight, obese, or severely obese groups over time were more likely to develop a disease of the inner lining of blood vessels known as endothelial dysfunction.
Williams said the research findings showed a gradient, where "the more different you are from normal, the worse your function".
The study said the link between childhood obesity and the disease was an important finding as endothelial dysfunction had been independently linked to an increased risk of heart disease and death.
"Childhood obesity sustained into adulthood may contribute to an increased risk of cardiovascular events [as a result of the condition]."
Williams said the fact the prevalence of obese and overweight children was on the rise combined with findings linking this to heart-health in later life highlighted a serious problem.
"This means we are facing a real time-bomb in terms of the potentially enormous burden of ill-health in a substantial proportion of our population."
While Williams said reducing one's weight could help reduce the risk, he couldn't say this conclusively.
"Since we don't know if you can turn it around, it's best not to become obese as it's very difficult to change that substantially."
The latest New Zealand Health Survey showed 11 per cent, or one-in-nine Kiwi children aged 2-14 were obese; a rise of 3 per cent over the last decade.
A further 21 per cent of children were also considered overweight, but not obese.
Children living in the most deprived areas were three times as likely to be obese as those living in more affluent areas.
Williams said this study, combined with others on the issue of obesity, served to highlight how important it was to develop strategies to prevent obesity quite early - "potentially from birth".