Overseer has been improved and an independent review has proven its fit for purpose.
The farm pollution management tool helps farmers use fertiliser and other inputs more efficiently, estimates nutrient loss and is used by regional councils to help inform regulations around water quality.
A report in 2018 by the Parliamentary Commissioner for the Environment said Overseer was flawed, opaque and open to gaming by farmers.
In 2021, an independent science advisory panel backed those concerns, finding Overseer was not designed to accurately estimate nutrient loss.
That prompted a redevelopment programme carried out by the Ministry for Primary Industries and Ministry for the Environment.
Overseer spokesperson Alistair Taylor said some parts of the tool have been completely overhauled.
"Over the past two years we've worked alongside scientists from AgResearch, Plant & Food Research, NIWA and Manaaki Whenua Landcare Research to look at the areas of the science which were identified as potentially needing some change.
"From there, there were five main different work streams, for a couple we concluded that actually there was nothing that had to change and there was a couple in particular in the crop space that needed some work."
Taylor said the crop side of the tool has been completely overhauled.
"When the cropping module of Overseer was developed there wasn't much New Zealand specific science but now there is so that's all been updated."
The changes were independently evaluated by a technical advisory group set up to establish and review Overseer.
Overseer chief executive Jill Gower said it confirmed the tool was now fit for purpose.
"The evaluation shows Overseer is performing well against measured losses of nitrate, with the tool rated as 'very good' for grazed pastures, and 'satisfactory' and 'good' for crop systems.
"The science programme has re-affirmed OverseerFM's role as a useful decision support tool that allows farmers and growers to make more informed decisions about their farm management practices, boost their productivity and profitability, and improve their environmental impact."