The owners of widely criticised nutrient management programme Overseer have assured MPs they have a plan to address the problems linked to it.
The Ministry for Primary Industries, the Fertiliser Association and AgResearch own Overseer.
They briefed MPs at a select committee yesterday.
The programme was designed to help farmers assess nitrogen and other nutrient losses from their farms; however, regional councils are now using it as well to set nutrient discharge levels in their land and water plans.
Overseer has been widely criticised by farmers, who said there was no consistency with the programme.
The government has responded by increasing funding to make changes.
MPI director of resource policy David Wansbrough told MPs the changes being made were around its use as a regulatory tool.
"The first is quality assurance, the second is usability. Third is its ability to adopt new farm practices and new technologies as they come on.
"The fourth is interconnection with other software and decision-making tools.
"The fifth one is to adopt some business focus and business disciplines into the process of developing the software and the sixth area is a sustainable funding model."
He said it was the only tool available to predict losses of nutrients into the environment on a farm-by-farm basis.
"Although it wasn't designed [as a regulatory tool], any attempt to regulate nutrients or greenhouse gas emissions from farms would need something like Overseer, so we are trying to make sure we improve it as a regulatory tool and address all of the issues that we need to address, because in some ways there is no alternative.
"People who use it - we hear quite a lot of frustration with it, but also there's quite a lot of willingness to make it work."
MPs raised their eyebrows when Mr Wansbrough said not all regional councils would use it as a tool.
They questioned what the councils would use instead and asked whether there was national consistency for water quality management, to which he replied:
"Every catchment is different. The science is different, the economics is different, the policies are different.
"Waikato - one big catchment with one big river. That's totally different from Canterbury, with lots of little rivers with different catchments that are not connected, so the national policy approach is to allow catchment based decisions."
He said in Taranaki, for example, the focus is on riparian planting, and in Canterbury, the priority is measuring nutrients on every farm.