"Due to Tip Top going on strike there is limited bread available. We hope to have a full range soon," the signs read.
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Countdown spokeswoman Charlotte Mee confirmed "supply issues" were affecting their stock.
"Bread is always incredibly popular at any time of the day but unfortunately at the moment we're experiencing a few supply issues in the Upper North Island for some brands of sliced bread.
"There are plenty of buns, loaves and other bread products from our bakery and they're almost always available for customers as we bake throughout the day based on demand in each store."
The shortage is linked to industrial action by more than 100 FIRST Union members at George Weston Foods' Tip Top bakeries in Otahuhu and Wiri.
The strike action meant much of the North island faced potential bread shortages, Stuff reported.
"Tip Top bakery workers are fighting to put bread on their own tables after years of negligible pay rises and no recognition of the family time they have to sacrifice to enable the company's 24/7 operation," union spokeswoman Anita Rosentreter told Stuff.
George Weston Foods general manager of baking Mark Bosomworth said the strike action meant the company was only likely to produce half its usual bread production on Tuesday and Wednesday, affecting North Island supply.
Many customers would notice a slim pickings on supermarket shelves but Wellington and South Island supplies were unlikely to be affected.
The company was disappointed with the union's action. Many of the claims had been settled.
"We pay competitive rates, we provide good training and we provide a safe, modern work environment for our staff," he told Newshub.
