"[It] is of course disappointing, but we also understand that sometimes change can be tough."
Countdown said reusable bags were now on sale from 15c.
"On the whole we've found customers are really supportive of the change away from plastic bags and the majority of customers are already remembering to bring their own bags when they shop with us."
A spokeswoman for rival supermarket chain Foodstuffs said the issue had not extended to any of its network stores.
"It's not a widespread issue at Foodstuffs stores which have currently gone plastic bag free," the spokeswoman said.
"We think this is down to the fact that we have communicated clearly with our customers about the switch to reusable bags and that we've given away millions of bags to help them adjust to the change."
Foodstuffs operates Pak'nSave, New World, Four Square and Fresh Collective.