"In the first instance, we want to work with the food industry on voluntary measures that support the health of New Zealanders," Clark said.
"This is a great move by Countdown ... Countdown's move is exactly what we want see. I hope other companies will follow their example."
However, the decision was not as popular in other areas of the food and beverage industry.
Before the change the nation already had some of the world's strongest energy drink regulations, New Zealand Beverage Council spokesman Stephen Jones said.
And strict limits had already been imposed around advertising and packaging, he said.
"We believe current regulations are working well, with government research showing the majority of children are not consuming energy drinks in large quantities."
The NZBC had concerns the ban could create desirability of energy drinks among young teenagers, given the tendency to desire what you can't have, Jones said.
Meanwhile, New Zealand Dental Association sugary drinks spokesman Dr Rob Beaglehole applauded Countdown for imposing the restriction.
"Countdown needs to be praised from doing the right thing here.
"It's voluntary for them to set this age restriction, but significantly it sends the right signal and we thank them for listening and for leading the way."
In the United Kingdom, Sainsbury's, Aldi, Asda and Waitrose all ask teenagers for ID when buying energy drinks - teens must be 16 years old.
Kiri Hannifin, Countdown's general manager of corporate affairs, safety and sustainability, said support from the public on the move was far-reaching.
"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 move from Countdown would be a beneficial one for children and teenagers, public health advocate Dr Lance O'Sullivan said.
Reduced access to energy drinks was a step in the right direction to help children have better health outcomes, he said.
Countdown's competitor, Foodstuffs, which operates New World and Pak'nSave, shared the same stance as the NZBC.
Head of corporate affairs Antoinette Laird said it had been focusing on education with children and parents.
"To date, more than 150,000 youngsters have been through the in-school 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."