Agriculture Minister Bridget McKenzie said the fees outlined were only in a draft and growers would have the opportunity to submit comment.
But the citrus industry says Senator McKenzie has signed off on the proposals and they are unhappy that the proposals even made it this far.
The industry said if the Agriculture Department was worried about cost recovery, then the department should look at becoming more efficient.
Citrus Australia said the move would cost the average grower $30,000 before they had exported a single carton.
On October 11, the Federal Department of Agriculture released its proposed fees and charges for export certification for the next four years.
Citrus Australia CEO Nathan Hancock said he was astonished at the size of the increases for a service in which the government had a monopoly.
Price rises for growers included a 277 per cent rise in tonnage charge for protocol markets from $1.30 to $4.90 per tonne and a 277 per cent rise in tonnage charge for non-protocol markets from 65 cents to $2.45 per tonne.
Mr Hancock said the proposed fee structure did not have support from Citrus Australia and has called for a detailed and transparent examination of the program costs.
“At a time when we are suffering the worst drought in living memory, the government is increasing charges on our growers by exorbitant amounts,” Mr Hancock said.
“For the average grower that wants to export, the proposed costs will equate to around $30,000 per year before they have even exported a single carton. They will then be charged more than $250 per container to export.
“The Federal Coalition claims that it wants to grow Australian agriculture and support its farmers during the drought, but these price rises show these claims lack all sincerity.
Mr Hancock said the Department of Agriculture had effectively ignored the advice of CitrusAustralia and other representative bodies.
“In March 2018, we provided a detailed submission to government outlining our concernsbut clearly the department has disregarded everything we wrote,” he said.
Senator McKenzie said Department of Agriculture is currently reviewing its cost recovery arrangements to ensure sustainable funding of export services into the future.
She said it was important that fees and charges were reviewed regularly and reflected the actual cost of delivery.
Consultation closes on December 10.
For more details go to haveyoursay.agriculture.gov.au