It’s officially citrus season but one vitamin-packed treat could be missing from the fruit bowl.

Mandarins are in short supply with one major retailer selling out of the lunch-box favourite in some stores.

This week supermarket giant Countdown sold out of the popular easy-peel mandarins online but some stores had a plentiful supply.

A spokeswoman for the supermarket said the supply of mandarins would be a challenge this season with ongoing bad weather.

 “We do expect mandarin supply to continue to be a challenge with steady rain in the growing regions, and the weather forecast expecting this to continue for the rest of the week,” a Countdown spokeswoman said.

Flooding and continued heavy rain and slips causing road blockages were to blame, said President of United Fresh NZ Jerry Prendergast.

Gisborne was the supplier of all citrus fruit at this time of the year and the region had been hit hard with heavy rain and floods.

“Gisborne has had rain challenges in January and February but despite that, the citrus crop had performed well,” Prendergast said.

 “But since then it has rained constantly and the ground is exceptionally water ladden - it is quite shocking.”

Prendergast said surface flooding and sodden orchards meant growers couldn’t get out to pick the last of the season’s crops.

A major slip also blocked the main route to Auckland.

Trucks with citrus fruit had to detour to Taupo before making their way up to Auckland.

“All of these things cause gaps in supply,” Prendergast said.

Mandarins were also susceptible to clear rot which is where water ladden fruit has a shorter shelf life because of disruption to spray programmes.

Prendergast said there was some good news for citrus lovers - and other ways to get a shot of vitamin C over winter.

Shoppers are being urged to choose alternatives to weather-affected crops such as kumara and mandarins if they can't find their favourites. Photo / File

“Gisborne has a great crop sitting on the trees of navel oranges so we will see these from the end of July for a couple of months.

“We also have a few Australian oranges around until then.”

Mandarins weren’t the only casualty of terrible weather Prendergast said.

About 60 per cent of kumara crops were ruined during floods in Northland so stock was low and prices high.

“All of the kumara crops are picked at the same time in January, February and the first part of March so the whole season’s supply was affected by floods,” Prendergast said.

“The crop rotted in the ground before they could pick it.”

Kumara available at the moment was from the small amount growers were able to save.

“This won’t be forever, there are just these gaps and challenges,” Prendergast said.

“People will need to make other choices such as parsnips, beetroot and pumpkin. There are a lot of other fabulous choices out there.”