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University of Otago human nutrition researcher Dr Lisa Te Morenga says the situation was made worse by the supermarkets running losses on junk foods to bring in customers.
An example of this was a supermarket chain in Dunedin last week selling chocolate bars for 69c.
The latest Statistics New Zealand food price index showed in the year to the end of May, fresh milk prices were up 11.1%, the highest on record, and vegetable prices up 8.7%, while the price of ''confectionery, nuts and snacks'' was down 4%.
York Place Pre-School and Nursery head teacher Yvonne Baynes said the rising price of healthy foods meant ''kids are getting fizz rather than milk''.
''Our lunch-boxes are full of potato chips and Roll-ups because they are so much cheaper than fruit and vegetables,'' Ms Baynes said.
Apart from making life tougher for parents, rising prices were also adding to the preschool's costs, as it provided morning and afternoon tea.
The fact milk was now too expensive for many parents meant the preschool was giving its children milk twice a day.
Dr Te Morenga said it was disappointing supermarkets promoted unhealthy foods so heavily.
''They take a loss on those foods, but they don't take a loss on healthy foods.
''I personally would love to see supermarkets being told they just cannot heavily discount junk food like that and take them on as loss leaders.''
The temptation was particularly hard for ''hungry, growing teenagers'' faced with a decision on how to spend their pocket money.
Research showed there was a connection between the cost of both unhealthy and healthy foods and obesity rates - particularly in children.
''The changing prices of food have a real impact on the choices made by people on low incomes.''
She also supported introducing taxes on sugary drinks.
''We need to set some ground rules as a society to say these are the foods we don't want you to be spending your money on.''
A Countdown spokeswoman said it ran specials across its ''full product range''.
''We work really hard to deliver cheaper prices on a variety of groceries because we know that's important to our customers,'' the spokeswoman said.
Its prices on fresh produce had increased at ''well below the national average'' over the past five years, she said.
A spokeswoman for Foodstuffs, which runs New World and Pak'n Save supermarkets, gave a similar response.
''No single product or group of products is specifically used to loss lead.
''Each week, an appropriate mix of products are provided on special to meet our customers' needs,'' the spokeswoman said.
Neither company accepted any responsibility for rising obesity rates.