Mr Malcolmson said the company had sourced Bonita bananas from South America, which normally made up only a small number of its banana stocks, to alleviate the shortfall.
He said he could not guarantee a constant supply of bananas in stores.
Countdown sourced its bananas from the Philippines and Ecuador but was expecting some impact as a result of the shipment delay.
Rotorua Pak'nSave produce manager Steve Matthews said they did have bananas in full stock after running low during the week.
"We must be almost out the other end and back to normal.
"The shortage has also effected pawpaw and pineapples," he said.
New World Rotorua produce manager Michael Hutchins said they had enough bananas in stock to make it through the day but had recently sold out of bananas by 5pm or 6pm.
"By this Thursday we should hopefully be fully stocked and are hoping to put on some specials."
Mr Hutchins said between 10 and 15 people had asked about the shortage in the last few days.
Additional reporting by Otago Daily Times and Hamish McNeilly.