A study of 2143 children in the Hunter Region found nine in 10 school lunchboxes contain junk food.
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Only one in 10 lunchboxes contained "core foods", which was described as "minimally processed foods recommended in Australian dietary guidelines".
The University of Newcastle research found that parents can be supported to make "simple swaps to what they pack in lunchboxes to make them healthier".
The research found these healthy swaps "don't need to cost any more or take any more time to prepare".
Researcher Matthew Mclaughlin, a public health PhD candidate, said lunchboxes "currently contain an average of 3.1 discretionary food serves".
These include items like cake, chips, muesli bars and lollies.
The researchers pinpointed barriers that parents face in packing a healthy lunchbox for their kids.
"Overall, parents told us that they have a lack of time, so they wanted convenient foods," Mr Mclaughlin said.
Beforehand, parents didn't always have the knowledge of suitable swaps, such as pikelets for cakes.
"So we provided them with a bank of ideas and example swaps," he said.
"Parents wanted swap ideas to suit what their kids wanted to eat and different child preferences, including fussy eaters."
Parents sought swaps that were not more expensive. The research showed exactly this - swaps could be done without an increase in cost.
The research was done through the university's SWAP-IT program, which reduced the amount of unhealthy foods being packed each day.
Alison Brown, a PhD candidate in the School of Medicine and Public Health, said healthy swaps included popcorn for chips and fresh fruit or vegetables for fruit strings.
"These swaps don't have to burden time-poor parents. A typical lunchbox costs about $4 to pack," Ms Brown said.
The SWAP-IT program was designed to support parents to make "simple, tasty and healthy swaps, without costing parents an extra cent".
Parents also had concerns around food safety, such as keeping food cold, so the program provided them with ice bricks.
Dr Jannah Jones said parents often get blamed for packing unhealthy lunchboxes.
"But we listened to parents and heard about their challenges," Dr Jones said.
"They told us they needed swaps that were quick, easy and food-safe.
"So we didn't start asking parents to cook Michelin star meals. Instead, we gave them simple and frugal swap ideas directly to their phones".
Notifications were sent to parents' phones through a school communication app.
"Two-thirds of schools use such apps. These notifications provided practical swap ideas directly to parents."
She said 84 per cent of parents liked receiving these swap ideas as notifications.
Mr Mclaughlin said supporting rather than blaming parents was "the key to success".
"Ultimately, the aim of swapping to more nutritious foods is not only to support the kids to be healthy, but also to support their learning and behaviour in the classroom," he said.
"We also know that kids who eat healthy foods are more likely to eat healthy foods as adults."
Dr Rachel Sutherland, an expert in chronic disease at the University of Newcastle, said the foods that children consume at school account for 40 per cent of their daily energy intake.
"It is linked to their ability to concentrate and engage at school and ultimately their learning and academic outcomes," Dr Sutherland said.
She added that it was strongly linked to short- and long-term health including risk of tooth decay, heart disease, diabetes and development of some cancers.
"What we feed our children at school matters for both their school and health outcomes," she said.
Three serves of food that should be consumed only sometimes were in the average lunchbox each day.
"This means that 40 per cent of a lunchbox is made up of 'sometimes foods'.
"But making small changes in a lunchbox everyday, in line with the Australian dietary guidelines, can make a massive difference to children's health at a population level."
Mr Mclaughlin said the recipe for a healthier Australia had "multiple ingredients".
"One ingredient is regulating junk food adverts, another ingredient is supporting parents to pack healthy school lunchboxes. The quality of ingredients and how they're mixed matters."