Banana bread replaces the scarce fruit at Countdown Newtown, Wellington as the banana shortage stretches on

The nationwide banana shortage has hit Wellington with supermarkets selling out of the scarce fruit over the weekend.

The country's two major supermarket chains, Foodstuffs and Progressive, have been reduced to about 80 per cent of normal supplies after a ship from Ecuador carrying bananas broke down about three weeks ago.

Both chains said the supply from the Philippines remained unaffected.

The last time New Zealand had a banana shortage was March 2014 when bad weather affected growing conditions in the Philippines.

The shortage hit weekend food shoppers in Kilbirnie on the weekend, with both the Pak 'n Save and Countdown in the suburb selling out. Countdown in Newtown has also had empty shelves.

Foodstuffs spokeswoman Antoinette Laird said supply was still being rationed due to the shortage.

"This means in some cases – as happened at Pak 'n Save Kilbirnie late yesterday – the odd store will run out," she said.

Laird said bananas were back in stock at Pak 'n Save Kilbirnie as of Monday.

Foodstuffs' produce team had confirmed supplies should be back to normal by the beginning of next week.

Foodstuffs owns the New World and Pak 'n Save chains and Laird said each supermarket was managing their own stock levels and there were no reports of widespread shortages at the company's Wellington stores.

Countdown spokesman James Walker said the volume of bananas sold last week was down less than 20 per cent on the same week in 2014.

"There are still plenty of bananas around, only a little fewer than ordinary," he said.

The limited stock was being rationed out in supermarkets on a daily basis meaning some supermarkets – such as Countdown in the Wellington suburb of Newtown – were selling out by the afternoon.

Neither customers or stores had registered any complaints about the shortage, he said.

"Countdown stores will continue to manage supply levels as best as they can. We still expect normal volumes of bananas to return next week," Walker said.

Wellington Zoo spokeswoman Charlotte Whitelaw said zoo animals had been unaffected as they only ate All Good Fairtrade bananas, which came from a different source.