A soil scientist who was involved in the initial development of the controversial nutrient management system, Overseer, agrees with critics who say it is being misused.
The computer software programme was designed to help in the assessment of nitrogen and other nutrient losses from farms.
Regional councils are now using Overseer as well to set nutrient discharge levels in their land and water plans.
Independent soil scientist and fertiliser consultant Doug Edmeades was a National Science Leader with AgResearch in the late 1980s and early 1990s when the Overseer concept was born.
He said the Overseer programme is world class - no other country has such a tool.
But Dr Edmeades said it was not being used in the role it was designed for and that it had never been intended to be used as a regulatory tool.
He feared misusing it would throw up inaccurate and misleading results.
"It was designed to do what is analysis, so you'd set up a farm in Overseer and look at the impact of different farm management practises, on, say, nitrate leeching.
"The problem I have is when you put it into a regulatory environment then you run in to all sorts of problems.
"People who are using it need to appreciate that it comes with errors, and, at a minimum, the error in the predicted nitrate leeching is plus or minus 30 percent, but it can be up to 100 percent if you get some of the input data wrong, and that's not an obvious thing.
"Things like soil texture at depth is not obvious to anyone walking over a farm and we don't have that sort of information at the farm scale that we need it," he said.
"My worry is that if you put Overseer into a regulatory setting, by that I mean if regional council writes a rule saying farming is permitted, if the nitrate level as measured by overseer is less than 30.
"As soon as you do that, you're inviting argument about, is that the right input data to be using on that farm etc, because of the errors."
Dr Edmeades said that could lead to a lot of legal challenges from farmers.