The plan has been greeted by suggestions that perhaps the money should be flowing the other way.
FarmersWeekly said KiwiRail had told farmers along the main trunk line in May they would be allowed just one crossing each, giving them 30 days to decide which one would be retained.
Farmers were told KiwiRail wanted to close many of the 1287 rail crossings on private land because of safety concerns.
KiwiRail today told the broadcaster it was trying to formalise crossing rules for health and safety reasons and the charges could eventually apply to about 3500 crossings nationwide. Formalising the policy, previously only loosely enforced, would ensure they were safe, documented and costs correctly charged, KiwiRail said.
Mid-Canterbury dairy farmer Chris Ford told FarmersWeekly he expected farmers would take a hard line on the fee.
"As farmers we pay for the underpass and we don't have district or regional councils charging an annual inspection fee to go under or over a road so what gives KiwiRail any right to charge this on farmers' own land?
"There's a private property access issue here and farmers would in turn have a right to charge KiwiRail for access on to their properties," Ford said.
It would be a test of the charges when the accounts were sent.
"What will they do if we don't pay them?"
He was also upset at KiwiRail's plan to hike rent on unproductive land leased to farmers.
Under the agreement negotiated with Federated Farmers it will pay nothing to farmers who provide it with access to rail land or land used to store rail materials.
Ford estimated he would be charged $9600 a year under the new policy for 12ha.
"It's a bit of dryland that doesn't do anything. It wouldn't earn the rental increase. It's not practical to develop and while there is limited grazing available at certain times of the year we have to maintain the land, fences and pest control all year round.
"All I see from this is that KiwiRail will set a precedent and drive up the value of other leasehold land."
KiwiRail last year told farmers of its review of existing property leases on land next to the rail corridor. Rental increases proposed were threefold in some cases.