Some 44% of Country Land and Business Association members surveyed have experienced a reduction in the availability of migrant labour over the past year.
Nearly 90% of respondents said they had tried to recruit locally but the majority found it difficult to fill positions with British workers.
Restricting access to migrant workers once the UK leaves the EU would negatively impact more than half of rural businesses, said the CLA.
See also: Brexit has major rural implications
The rural organisation, which represents landowners, farmers and rural businesses, revealed the results at the South of England Show on Thursday (8 June).
One in ten CLA members employ migrant workers in managerial positions, with almost a quarter of respondents saying they worked in skilled roles.
The survey revealed that although overseas labour peaks during harvest months, workers are employed all year round within rural businesses.
CLA senior economics adviser Charles Trotman said: "Our survey shows that rural businesses employ thousands of migrant workers who are vital to the rural economy."
Most CLA members employ fewer than 10 migrant workers per business although others employ many more, suggests the survey.
"The government must provide certainty that after Brexit there will still be a flexible, skilled and secure workforce in order for rural businesses to plan for the future," said Dr Trotman.
To support the already acute shortage of labour a new seasonal agricultural workers scheme should be introduced immediately, not after the UK had left the EU.
Dr Trotman said: "The government must also confirm the status of EU migrant workers in sectors such as food processing, horticulture and tourism already resident in the UK."
Despite the hung parliament, the CLA says it remains confident the government can secure a Brexit deal that works in the long-term interests of the rural economy.
But it says that politicians from all side must work together to secure priorities that extend well beyond Brexit.
Rural businesses need economic stability and confidence to grow and create jobs – as well as to build homes and infrastructure for rural communities, says the CLA.
CLA president Ross Murray said: "Achieving positive outcomes on these issues remains the CLA's single minded focus and we will work with all sides in this parliament to achieve these things."
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