Some British retailers and wholesalers have been forced to switch to sourcing oranges from South Africa and South America early after last month’s catastrophic floods in eastern Spain left farmers struggling to harvest and ship their crops.

Companies in the UK have moved to buying fruit from the southern hemisphere several weeks earlier than in a typical year to prevent gaps emerging on supermarket shelves and amid fears over the quality of Spanish produce.

Persimmons, also known as sharon or kaki fruit, have been affected even worse than oranges by the flooding as they are more delicate than citrus, analysts and industry insiders said.

The Valencian branch of Asaja, Spain’s biggest farming association, has estimated that the floods have resulted in losses of more than €1bn for the region’s agricultural sector.

“The damage is catastrophic in terms of output, cultivated fields, agrarian infrastructure, agricultural machinery and vehicles, livestock farms and nurseries – and in terms of the lands lost as entire fields have disappeared,” it said.

Exports have also been affected by damaged motorways and rural roads as well as a recent blockade by French farmers protesting against the signing of a trade deal between the EU and Mercosur.

However, Fepex, the Spanish federation of associations of producers and exporters of fruits, vegetables, flowers and live plants, said exports through France had now resumed.

One agricultural source said it was still too early to assess the full extent of the damage: “The streets are being cleaned up but the fields are always the last thing that gets cleaned up,” they said. “We’re talking about a lot of rural roads and they’re just aren’t the resources.”

The source added: “We’re in full picking season here and we were already expecting the harvest to be a bit lower, so when you add in [the floods], quite a lot of citrus has been lost.… We’re right in the persimmon season now and that’s what’s been most affected.”

One big UK retailer said it had been forced to buy oranges from South Africa as it was so difficult to source citrus from Spain because of the hold-ups on affected roads and warehouses as well as damage to crops.

Jason Glass, the managing director of wholesaler All Greens at London’s New Covent Garden market, said that the wholesale price of oranges had risen more than 30% immediately after the floods because of interruption to supply, although that has since reduced as competition from the southern hemisphere has kicked in.

Difficulties for UK buyers have been exacerbated by the extra checks caused by Brexit, which had already put up costs and lengthened delivery times, Glass said.

Cindy van Rijswick, global strategist for the fruit, vegetables and floriculture sectors, at Rabobank, said the industry had been expecting supplies of oranges to be below the four-year average but higher than last year, while easy peeler prices had already been high before the flooding in anticipation of a poor season.

She said: “It is not clear yet how much additional pressure the floods will have on supplies.”

Not all farms in Spain have been equally affected, however. One large retailer said it had “no major issues” with supply as the location of its farmers meant they had seen only minimal impact on crops as citrus is grown well beyond the Valencia region.

One citrus industry source told the Guardian the main problem remained a logistical one of getting the fruit off the trees, packed and then loaded on to lorries bound for the UK and other parts of Europe. The citrus crops as a whole, they said, had weathered the rains and floods of recent weeks in Valencia and beyond.

“Even in the parts of Valencia that were hit hardest by the floods, people are getting in and seeing there’s quite a lot of fruit that can still be saved,” they said.