Dr Tony Jewell noted that, although five daily portions of fruit and vegetables have been shown to reduce the risk of heart disease, stroke and some cancers, the average Welsh adult eats only three portions, with many eating far fewer.
In a nation with soaring obesity rates, the latest consultation - billed to be the largest of its kind in the UK - will seek to enable the public to shape the future of food in Wales.
"The future of our national diet is incredibly important for everyone living in Wales and that is why the Welsh Assembly government is launching this public debate," said Dr Jewell.
"We must ensure that healthy food is more accessible to the people that need it most."
Lindsay Kearton, senior policy officer at the Welsh Consumer Council, said that access to affordable healthy food is "fundamental" to helping people eat a balanced diet.
"Reconnecting people with the food supply chain will be an important step towards helping consumers to make choices that help to both support the local economy and look to the wider welfare of the planet," she added.