"Every year we delay the collection of data identified as a significant gap, we commit New Zealand to flying blind in that area."
Just as importantly, a lack of good oversight could be costing the country in the form of poorly designed policies or irreversible damage.
"Further, the costs are not just environmental – they have real consequences for the economy, society and our wellbeing."
In a 100-page review released today, Upton recommended overhauling the Environmental Reporting Act to have a clearer purpose, with core environmental indicators to form the backbone of reporting.
He also suggested a new standing science advisory panel be set up, that the Government be required to formally respond to each new stocktake, and that a comprehensive monitoring system be established to fill the data gaps.
The Environmental Defence Society backed his calls.
"Overall we are concerned at the obvious deficiencies in our environmental reporting system identified by the Commissioner, most of which come down to underfunding," its chief executive, Gary Taylor, said.
"We can't manage what we don't know so Government really does need to get on with implementing the suite of recommendations."
Local Government New Zealand president Dave Cull said the lack of a coherent system had long been a bugbear for councils, which collectively spent $40m on data collection and reporting each year.
"Right now data is being cobbled together from a range of sources, with mixed methodologies, and that's failing to deliver a clear national picture."
The two departments charged with managing the system – the Ministry for the Environment and Stats NZ – acknowledged improvements were needed, adding the recommendations could be used to build on what changes had already been made.
They included drawing on "citizen science" from new community partnerships, along with satellite data.
"Environmental reporting is all about putting robust, independent, rigorously checked information into the hands of decision-makers and the wider public," Government Statistician Liz MacPherson said.
"We should always be open to new ways of doing that."