Industry group Horticulture New Zealand says the regional fuel tax is leaving some Auckland fruit and vegetable growers ten of thousands of dollars out of pocket.
The 11.50 cents a litre tax that was added to fuel prices on the 1 July.
Farmers should be able claim back the regional fuel tax for on-farm vehicles and machinery using diesel.
However, Horticulture NZ chief executive Mike Chapman said the rebate system was far too complicated and costly.
Mr Chapman said on 9 October an online rebate system was launched by the New Zealand Transport Agency, but the situation had not improved.
Growers were required to claim for each individual farm vehicle or piece of machinery, but that was simply not practical as some businesses could have up to 100 different pieces of farm machinery, he said.
Growers who wanted to make monthly claims were not able to do so, he said.
'What we're finding is growers are saying 'it's actually too complex and hard for us to claim, we'll just bear the loss'... and some of these growers are looking at 40, 50, 60, $100,000 that they're going to bear in fuel tax they shouldn't be paying mainly because it's hard to claim,
"If they are going to claim they're probably going to have to employ someone to actually do the claims... so it's just wrong," he said.
Mr Chapman said it was clear that when the regional fuel tax legislation was passed it did not apply to machinery and tractors used off road.
"They should be exempt, it should be as simple as that and that's what we submitted when the bill went through parliament... and we weren't listened to," he said.
Mr Chapman said it was unfair that the government had been holding onto the growers money for three months not paying interest and if growers weren't going to make a claim "the government's getting free money".
Figures from the New Zealand Transport Agency show of the 39 requests for rebates dealt with so far - 25 have been approved and 14 declined. The total amount paid out is about $450,000.
The Ministry of Transport is currently reviewing the rebate system.
Transport Minister Phil Twyford said that work was expected to be completed next year.