But there are foods that can counteract those harmful effects, including oats, beans and potatoes, the researchers said.
Other counter agents include cooked and cooled rice, barley, legumes such as black beans and peas, and raw potato starch.
"These foods are important as they get down into your lower gut and basically serve as food for your gut bacteria," associate professor and study author Melinda Coughlan said.
" The gut bacteria ferment these food-producing metabolites that are anti-inflammatory.
"Now that we have shown that it is certain chemical compounds found in highly processed foods that play a role in chronic kidney disease, we can look to make alternative food formulations or functional foods aimed at dampening the body's response."
The researchers said processed food has become a diet staple in many parts of the world, but the exact mechanisms by which the food impacts health is in need of urgent further research.
Coughlan said her new study was an important step towards understanding that issue.
"Given the increasing interest in the effects of processed food on health, we believe that these findings represent an important step towards understanding and countering the detrimental features of the modern diet," she said.
"Dietary change, as with most behaviour change, can be difficult to maintain long term, but by adding more foods high in resistant starch fibre and steaming and stewing cooking practices we can help dampen the harmful effects."
Other processed foods that tend to contain AGEs include bread, bakery products, and confectionery.
Chronic kidney disease affects 10 per cent of the global population.
