The grocery giant, which operates New World, Pakn'Save and Four Square brands, had sourced Bonita bananas from South America, which normally make up only a small number of its banana stock, to alleviate the shortfall.
"We have people on the ground endeavouring to get as many bananas as we can but when a whole shipload gets turned back on top of a shortage through weather conditions it make it very hard... but we will get through," Mr Malcolmson said.
He said bananas were not a big money earner for the New Zealand-owned company "it is a lead product and we like to have bananas on shelves 24/7".
But asked if customers could expect bananas to be on shelves 24/7, he replied "I can't guarantee that".
"It is depending on the logistics of how many bananas we can get though."
Peter Hendry, chief executive of MG Marketing, Foodstuffs' main banana supplier, said the supply of bananas for this week would be down 30 per cent due to the vessel breaking down.
A new shipment was expected to arrive in Auckland on Friday, with supply to retail expected to be back to normal from next Wednesday.
A spokeswoman for Australian-owned Progressive Enterprises, which operates Countdown, Fresh Choice and SuperValue brands, said "we'll be doing our best to manage stock centrally to ensure any impact to customers is kept to a minimum".
Countdown sourced bananas from both the Philippines and Ecuador but was expecting some impact as a result of the shipment delay.
Veggie Boys co-owner Marty Hay said the independent fruit and vegetable store notified its customers of the shortage this week.
The shortage had forced the store, which operates four outlets, to temporarily raise prices from $1.99 a kilo to $2.49 a kilo.
"We are getting through, it is tight. But customers have been very understanding."
