"New regulations mean our cigarettes are now stored in secure cabinets but the company decided to introduce its own measures across the stores that mean no one can actually see the cigarettes," a Foodstuffs spokesman said.
Rivals, Progressive Enterprises, owners of supermarket chain Countdown, insist they won't be following suit.
"We abide by all the new regulations and spent a long time discussing these with the Ministry of Health, but we have no plans at the moment to take further measures to keep cigarettes out of view," a spokesman for Progressive said.
However, many smokers are baffled by the move at the other supermarkets.
"Being handed a pack of cigarettes hidden in a bag makes me feel dirty," said one New World customer, a smoker who declined to be named.
"It is just another example of PC-madness."
The move is another blow for tobacco companies who have vowed to fight the Government's bid to cut smoking rates through higher taxes and ever stronger measures.