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Youthful-looking shoppers might also be asked to show ID at check-out.
The Australian-owned chain defines energy drinks as a sub-set of formulated caffeinated beverages, with added caffeine and/or added guarana as ingredients. This includes Red Bull, V, Monster Energy, Pure Energy and Berocca.
Drinks that are known to have high sugar - such as Mountain Dew, Coca-cola and Pepsi - are not included on the list.
The company confirmed yesterday that the ban was exclusive to Countdown in New Zealand and would not apply to its Woolworths chain in Australia.
Countdown Dunedin Central store manager Ron Andrew said it was early days but shoppers had generally accepted the new rule.
''None of our customers have been aggressively against the ban and we think we have a certain responsibility to ensure our children aren't able to buy products that they really shouldn't be using,'' he said.
He said sales of most of the listed drinks were mainly during the latter part of the week and were not to younger teenagers, in any event. He acknowledged, however, the inclusion of Berocca ''was interesting''. '
'It's generally regarded as a healthier option.''
Kiri Hannifin, Countdown's general manager of corporate affairs, safety and sustainability said the policy had been implemented following ''genuine concerns out there about the impact of caffeine and sugar on our kids''.
''We made our decision after engaging with health and education leaders, but also in talking with our team, many of whom are parents themselves.
''Across the board, we found communities of people who are seeking help to address New Zealand's high child obesity rates.''
The Countdown move had also been roundly supported by Health Minister David Clark, who said he hoped other companies would follow its example.
The Ministry of Health does not recommend energy drinks for young people because of the high amounts of caffeine and sugar. There have been warnings of the danger associated with high caffeine consumption.
Supermarkets in Britain, including Asda, Sainsbury's and discount retailer Aldi, have already introduced similar measures, requiring children to prove they are at least 16 at the time of checkout.
However, New Zealand beverage council spokesman Stephen Jones said it was an unnecessary step and a case of a ''solution looking for a problem''.
''Independent research from Food Standards Australia and New Zealand shows that energy drinks contribute less than 3% of the overall caffeine intake of young people aged between 9 and 15,'' he said.
''This low level of consumption is evidence that the existing framework around the sale and marketing of energy drinks is effective and that young people are consuming caffeine from sources other than energy drinks.''
Foodstuffs, owner of New World, Pak'n Save and Four Square markets, agreed it was a ''heavy-handed response to a problem that does not exist''.
''We care about our customers and their ability to decide what is right for them. Research shows people under the ages of 16 are not high consumers of these types of products. However, it is important to us that we provide customers with the information they need to make informed decisions,'' Foodstuffs said in a statement.
A Foodstuffs representative said the company's focus was rather on educating children and their parents on how to make better choices in general.
''To date, more than 150,000 youngsters have been through the in-school 'Food for Thought' programme with fantastic results. For example, we've seen a reduction of sugar consumption in excess of 50 tonnes with families who have taken part.''