A range of changes come into effect for Australian visa programs from July 1, including a 25 per cent increase in visa charges for working holiday makers.
The National Farmers Federation said the changes will make Australia up to five times more expensive than countries such as Canada, New Zealand and Germany and will turn away working holiday makers including farm workers.
"Any increased charges, anything that makes them have less money to spend ... they will take that into account," the federation's Fiona Simson said.
The changes will also bring the first British backpackers not required to undertake specified regional work to extend their stay.
Currently Britons must show they have done at least three or six months of 'specified work' to qualify for a visa extension, but from July 1 of 2024 they will not have to meet this requirement.
"We think regional Australia will miss out to the tune of potentially tens of thousands of backpackers," Ms Simson said.
A new wage threshold for temporary skilled migration means workers will need to be paid a minimum of $70,000 instead of $53,900, a figure which the federation says will rule out 84 per cent of agriculture workers.
Bill Bulmer from AusVeg, which represents 3600 Australian producers, said workers are already in short supply across the industry.
"The backpacker doesn't have to come and work on the farm any more," Mr Bulmer said.
"It becomes a problem for a lot of regions across Australia."
The agriculture industry is already facing worker shortages, a problem exacerbated at harvest time when working holiday makers are heavily relied upon.
Farmers warn further labour shortfalls will mean less produce.
"If you haven't got a workforce you either cut back on the amount of product you're growing or in some cases you go out of business," Mr Bulmer said.
"We're already thousands of workers short across the industry now."
Immigration Minister Andrew Giles said Labor is committed to improving wages and conditions for all workers, which includes a pay increase for those on the temporary skills shortage visa.
"Raising the TSMIT (income threshold) is an important step in delivering better pay for people working on Aussie farms," the minister said.
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