A major study into the health of Aboriginal and Torres Strait Islander children has found programs and policies to promote healthy weight should target children as young as three.

Lead researcher Katie Thurber from The Australian National University (ANU) said the majority of Indigenous children in the national study had a healthy body Mass Index (BMI), but around 40 per cent were classified as overweight or obese by the time they reached nine years of age.

"People who are obese in childhood are at increased risk of being obese in adulthood, which can increase the risk of cardiovascular disease, some types of cancer, diabetes, and arthritis," said Ms Thurber, PhD Scholar, from the National Centre for Epidemiology and Population Health at ANU.

Ms Thurber said the research found reducing consumption of sugary drinks and junk food from an early age could benefit the health of Indigenous children, but that this is just one part of the solution to improving weight status.

"We know that Indigenous families across Australia - in remote, regional, and urban settings - face barriers to accessing healthy foods. Therefore, efforts to reduce junk food consumption need to occur alongside efforts to increase the affordability, availability, and acceptability of healthy foods," she said.

Latest national figures show obesity rates are 60 per cent higher for Aboriginal and Torres Strait Islander peoples compared to non-Indigenous Australians.

In 2013, around 30 per cent of Indigenous children were classified as overweight or obese, and two thirds of Indigenous people over 15 years old were classified as overweight or obese.

Ms Thurber said improving weight status would have a major benefit in closing the gap in health between Indigenous and non-Indigenous Australians.

"Obesity is a leading contributor to the gap in health," Ms Thurber said.

"We want to work with Aboriginal and Torres Strait Islander families and communities, as well as policy makers and service providers, to think about what will work best to promote healthy weight in those early childhood years.

"We want to start early, and identify the best ways for families and communities to support healthy diets, so that all Aboriginal and Torres Strait Islander children can have a healthy start to life."

The research used data from Footprints in Time, a national longitudinal study that has followed more than 1,000 Indigenous children since 2008. It is funded and managed by the Department of Social Services.

Professor Mick Dodson, Chair of the Steering Committee for the Footprints in Time Study and Director of the ANU National Centre for Indigenous Studies, said Aboriginal and Torres Strait Islander children deserve the best possible start in life.

"This study shows just how important it is to support them, their families and their communities to provide a healthy diet and opportunities for physical activity," Professor Dodson said.

Ms Thurber said using the Footprints in Time study, researchers for the first time were able to look at how weight status changes over time for Aboriginal and Torres Strait Islander children, enabling them to identify pathways that help children maintain a healthy weight.

The research has been published in Obesity.