The chemical is used to make polycarbonate plastic, and is found in epoxy resins used to line cans to prevent corrosion.
The highest levels have been found in cans containing Edgell Corn Kernels and John West Tuna Olive Oil Blend, consumer watchdog Choice says.
It tested 38 samples of canned foods commonly found on supermarket shelves to conclude 29 had BPA levels that could be harmful.
Food-maker Heinz responded to the findings by announcing it would introduce BPA-free packaging for all its baby food brands.
"We welcome this move by Heinz and now call on the government to phase out BPA packaging for all baby foods and foods designed for toddlers and young children," Choice spokesman Christopher Zinn said in a statement on Thursday.
But the food and grocery council has rejected the findings, maintaining there is no evidence to suggest food packaged in cans containing BPA is harmful.
"There's no scientific evidence internationally that has shown any dangers to humans from BPA in canned products or bottles," spokesman Dr Geoffrey Annison said in a statement on Thursday.
"Products containing BPA have been subject to significant and rigorous investigations by leading world authorities and, in recent years, food regulators in the United States, UK and the EU have examined the latest findings and have determined that the use of BPA continues to be safe."
Amid public concern, big retailers and manufacturers began a voluntary phase-out of baby bottles containing BPA from July 1.
