KiwiRail is set to enforce a system of annual charges for private use of level crossings and underpasses that cross its network.
Farmers are the first group being targeted by the state-owned enterprise as it takes stock of a number of crossings around the country and ensures they meet appropriate safety standards.
KiwiRail said it was trying to formalise existing crossing rules for health and safety reasons and the charges could eventually apply to about 3500 crossings nationwide.
Formalising the crossings policy - which had previously been loosely enforced - would ensure that they were safe, documented and costs correctly charged, KiwiRail said.
It wanted to collect an administration fee of $350 per private crossing and charge an annual inspection fee dependant on the individual crossing.
The company would also require crossings to be maintained and that any crossing it considered dangerous be removed.
The main entry onto John and Helen O'Connor's drystock farm in Ngaere crosses the New Plymouth to Marton railway line which runs alongside State Highway 3.
Mr O'Connor paid KiwiRail a one-off access charge of about $300 when he moved onto the property about nine years ago.
He was not thrilled about paying an annual administration fee and inspection costs for a crossing he maintained himself.
"We'll I think that's a bit steep. I don't mind if they bring in a bit of tarseal and give us a bit of a smooth entry over the lines, but they've done absolutely nothing to the crossings.
"My wife's got a mini and it was starting to hit the rails so I had to supply the metal and build it up myself. So yeah, they don't give us anything."
Mr O'Connor did not think an annual inspection was necessary.
"I don't mind one inspection under the new health and safety legislation and perhaps they could tell us what signs we need to put up, but I think to inspect it every year is just over the top."
A level crossing connects two sections of Bill Gribble's Eltham dairy farm.
If KiwiRail wanted to charge him for it, that would have implications for townies too, he said.
"Well as far as I understand we are on a paper road so I guess they can't charge us for that because if they charge us for that they've got to charge every council a fee for going across any road the railway line crosses."
Mr Gribble also felt the charges were on the steep side.
"A $300 charge for administration seems very high to me. I think they are being a bit over the top with that. Inspections, yes, you could probably justify it for an inspection but are they going to do one every year, I very much doubt it."
KiwiRail said there were about 1300 public crossings on property owned by regional and local councils, NZTA, the Department of Conservation and ports.
There were also about 1350 private crossings over its network that it knew about which accessed farms, private homes and businesses. It estimated there were another 700 undocumented or substandard crossings.
Federated Farmers believed inspection fees would range from $300 for standard level crossings up to $900 for underpasses.
Its Bay of Plenty representative Daryl Jensen said farmers in his area were not happy.
"They are certainly aggrieved that there's now this yearly inspection fee that has to be charged when you know when an underpass has been in maybe just a couple of years or something. Maybe a yearly inspection but not a yearly fee for having that underpass there."
Mr Jensen said in general, farmers had a good relationship with KiwiRail and were not cavalier around rail lines.
"Farmers don't willy-nilly cross the railway lines with their stock and their vehicles, you know.
"They're out there looking for trains and I know there are certain areas where farmers communicate with KiwiRail if they're going to have stock going across a railway line just to make sure there's a window of opportunity to get stock from one side of their property to the other."
KiwiRail had recently increased the rent for land farmers lease next to rail corridors by as much as 350 percent in some cases and some farmers feared the new fees were just another revenue gathering exercise, Mr Jensen said.
In a statement KiwiRail said this was not the case.
"KiwiRail is not seeking to make money from this - it is a health and safety issue. The annual inspection and administration fee are charged on a cost-recovery basis.
"The fee covers costs for staff to maintain a legal agreement, and is needed to ensure users maintain the crossing to an agreed standard, meeting minimum health and safety requirements in areas including approach to the crossing, sight lines and signage."
KiwiRail hoped to have finalised its rail crossings policy - which would apply to all crossings on its network - in the coming months and make it available to the public.