Thousands of tonnes of fruit and vegetables are being left to rot in UK fields because of a shortage of pickers and packers in the face of continuing Brexit uncertainty.

Overseas workers, who account for the vast majority of the horticultural labour force, have been unwilling to come to the UK or have returned home early because of fears about their status in the event of a chaotic exit from the EU.

With farmers reporting a shortage of workers of 30% or more last month, some of those with autumn-harvesting crops including berries, apples and beans have been forced to leave their produce in fields and orchards. According to the trade journal The Grocer, some farmers are having to shut down operations six weeks early because they do not have enough workers.

Chris Chinn, a blueberry and bean grower in Herefordshire, said he would have to walk away from half his potential October crop because he only had half the workers he needed.

“The shortage of workers is the biggest threat to our business. Without staff to pick crops like beans, where we don’t have an automation option, then we cannot harvest them and they won’t be available on supermarket shelves.”

He said the farm had suffered shortages despite stepping up direct recruitment in eastern Europe and offering more perks, including higher bonuses for good pickers and improved accommodation with free wifi.

Another fruit farm in Herefordshire said last week that it had wasted 87,000 punnets of raspberries in just a fortnight because it was short of 100 pickers.

This year’s worker shortages are the latest in successive years of labour problems which began in 2013 when the UK government ended a seasonal workers visa scheme that enabled farmers to bring in pickers and packers from outside the EU.

That came ahead of workforce shortages across the EU as Polish, Bulgarian and other eastern European citizens, who had previously sought seasonal work in western Europe, are increasingly able to find jobs closer to home. The UK has suffered particular difficulties because of uncertainties about visa status, the fall in the value of sterling and headlines about poor treatment of immigrants.

The National Farmers’ Union found there was an overall 18% shortfall in the number of agricultural workers in August, even though businesses had tried to head off difficulties by recruiting up to 25% more people than usual.

Ali Capper, the chair of the NFU’s horticultural board, said she expected the shortfall to rise to at least 29% in September. She added that two or three businesses collapsed last month because of the problems.

She called on the government to expand a pilot scheme, which currently allows 2,500 non-EU workers to come into the UK for six months of work, to a national level.

“The shortage is driven by two things: government policy and the impact of Brexit,” Capper said.

“The UK is competing with Germany and Denmark and other countries. There are a lot of reasons why [workers] might not choose the UK.”

Uncertainty about ending freedom of movement and headlines about EU migrants no longer being welcome, together with the fall in the value of the pound – which has reduced potential take-home pay – had all put workers off, she said.