WA farmers are paying more than 200pc to operate their trucks than their commercial counterparts.
WA Farmers Federation (WAFarmers) transport and economics executive officer Ross Hardwick said the National Transport Commission (NTC) average cost recovery charge for a non-farming semi-trailer truck equated to 14c/km.
He said the cost of a farmer doing 10,000km in a semi-trailer truck was 34c/km, 239pc more than the NTC average cost recovery charge.
"Farmers' logistical freight task is effectively subsidising urban and major arterial road infrastructure and maintenance other than their own," Mr Hardwick said.
WA farmers are eligible for a 50pc concession on one truck of 8t or less on their property.
Mr Hardwick said the 50pc concession had become obsolete because many farmers were not using 8t trucks for bulk cartage.
WAFarmers will make a submission to the Planning and Infrastructure Department for a licence charge reduction on farm trucks of more than 8t.
"The average task for a farmer's truck is a lot lower," Mr Hardwick said.
"Half the time they are empty.
"Farmers probably wouldn't mind paying if they got the equivalent expenditure on the roads."
He said when the average freight-task ratio was factored in, it would highlight a further overcharging forced on farmers.
Farmers would need an 80-90pc concession on their truck registration to bring them in line with commercial freight task costs.
WAFarmers also will prepare a submission for the NTC's fourth determination on truck registration and diesel excise charges due in 12 months.
State transport ministers last week quashed the NTC's third determination proposal to significantly increase heavy vehicle registration.
Farm and trucking lobby groups, which have strongly rejected the NTC's recommendations, welcomed the move.
Australian Trucking Association (ATA) chief executive officer Stuart St Clair said the rejection was a great step towards transport efficiency and productivity.
"It's an acknowledgment by governments that an efficient trucking industry is vital to Australia's economic success," Mr St Clair said.
The ATA also is supporting a Productivity Commission inquiry into the efficiency and pricing of road and rail transport.
The report is due for release at the end of the year.
WA Planning and Infrastructure Minister Alannah MacTiernan said she hoped the inquiry would answer the uncertainties that have been created in the future funding of road infrastructure.
"In the past, the NTC determinations have provided the basis for recovering direct expenditure on roads and bridges from heavy vehicles," Ms MacTiernan said.
"The Federal Government has yet to explain how it intends to fund bridges on local roads for export freight access to inter-modal terminals."
Ms MacTiernan said a new source of funds for road and bridge repairs had to be found.