The tax, set to come into effect in July, will see people on working holiday visas taxed at 32.5 per cent from the first dollar they earn.
Northern Territory Chief Minister Adam Giles said he would raise growers' on-going concerns about the tax at the next meeting of the Council of Australian Governments meeting.
Katherine farmer Peter Marks hired Pacific Islanders to pick mangoes last year, with backpackers in the packing shed, but was “in a state of concern” about whether he would be able to find enough workers for the upcoming harvest.
He said it was likely that other growers would look to the Pacific Seasonal Worker Program to fill potential labour gaps caused by the backpacker tax.
“People are going to go where they can find labour, there is no two ways about that,” Marks said.
“There used to be times, 15 years ago, when crops were not picked because of not enough labour, and considering the industry has doubled since those times, I certainly hope we are not going to revisit those days.”
Another Katherine farmer has told ABC Rural he has lodged an application to have Pacific Islanders work on his farm this year because of uncertainty over the availability of backpacker labour.
Marks said workers from the Pacific Islands would likely spend less money than backpackers during their time in the Top End.
“The backpackers are also tourists. Last year we had a short break in between [harvesting] crops, and [the backpackers] went touring up around Kakadu, Litchfield Park and Katherine Gorge,” he said.
“They earned money and they went spending it.
“Pacific Islanders come here specifically to help their poor nations, which is really good, they get a chance to take money home, but they are not going to spend money like the backpackers, so that is going to be a bit of a loss to Katherine.
“I think the mix we have had in the past has been very beneficial to all,” he said