A farmer critic of the Overseer nutrient management programme has dubbed it the Novopay of the agriculture industry.
The computer modelling programme was designed to help farmers assess nitrogen and other nutrient losses from their farms.
Regional councils are also using Overseer to set nutrient discharge levels in land and water plans.
Officials agree the system has its limitations but say it is the only nutrient management tool they have.
The system is about to get a facelift, with a new management company and increased government funding.
South Canterbury farmer Jeremy Talbot doubts that's going to do much to improve a programme which he says is akin to the problem-plagued Novopay school payroll system which had to be rescued by the Government.
"It's totally unproven, it's never been used successfully anywhere else in the world, and recent reports from a professional Overseers' day in Canterbury said they need at least another $10 million in five years in order to get it to go anywhere near doing the job that the regional councils are demanding be done with it."
Mr Talbot says Overseer could be made to work by combining it with the European NVZ (nitrate vulnerable zone) system.