The NT government says the changes will mean the Top End mango harvest will be short of 1000 workers, with 70 per cent of the crop left to rot on the trees.
Growers, meanwhile, warn that fruit left on the trees would mean fewer mangoes making it to market, leading to higher prices for consumers.
Young backpackers are an essential labour force for Australian mango growers.
Home Affairs Minister Tony Burke has announced changes to the working holidaymaker visa program, reducing the cap on second-year visas from 57,000 to 45,000 and cutting third-year visas from 31,000 to 5000.
Backpackers will have to enter a ballot for the chance to remain in Australia for more than a year, meaning there will be about 38,000 fewer second and third-year backpackers than in 2026.
Mangoes are commercially grown in the Top End, Queensland, WA and northern NSW, with the NT providing about 50 per cent of the total crop, with harvest season running from September to December.
Trevor Dunmall, CEO of Australian Mangoes, told AAP the visa changes were a major concern for those who needed pickers and packers in the harvest season.
"There are huge benefits to the industry having a readily available work force," he said.
"We're really concerned that growers will not be able to pick the fruit and there will be less fruit available ... for Australian consumers and those consumers around the world who love Australian mangoes."
It was still uncertain what impact the changes would have on this year's harvest but 2027 was of great concern, Mr Dunmall said.
The way the federal government had handled the migration debate was flawed, he said, when backpacker fruit pickers did not intend to stay in Australia.
NT Agriculture Minister Gerard Maley said the Top End faced being nearly 1000 workers short for the mango harvest, leaving close to a million trays unpicked.
It would cripple the $128 million industry, which needed about 3500 workers during harvest, he said in a statement.
Around 70 per cent of the harvest would be left to rot, costing up to $27 million.
"This isn't just a number on a spreadsheet, it's fruit left rotting on trees, income lost by growers, fewer jobs in regional communities and less economic activity flowing through the territory," Mr Maley said.
NT Opposition Leader Selena Uibo called on her federal Labor colleagues to give the territory a carve-out.
"The federal Labor government will show a complete lack of regard for the Northern Territory if they do not give us a carve-out," she said.
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