In the study, just published in scientific journal Atmospheric Chemistry and Physics, a team led by Dr Kay Steinkamp and Dr Sara Mikaloff-Fletcher used an "inverse" modelling approach to estimate the amount of carbon uptake.
This was done by measuring the carbon dioxide present in the atmosphere at a network of sites, and then using high-resolution weather models to determine what parts of New Zealand the air had passed over before reaching the site.
Simulations from a land model, run by partners at GNS Science, and ocean carbon data, provided further information.
From there, the team calculated the best combinations of sources and sinks to match the data.
The project included data from Niwa's clean air station at Baring Head, near Wellington, its atmospheric research station at Lauder in Central Otago, and measurements taken from a ship that collects observations on a line between Nelson and Osaka, Japan.
"The inverse approach integrates information about carbon dioxide sources and sinks from atmospheric data, ocean data and models," Steinkamp said.
"The story the atmosphere is telling us is that there's a big carbon sink somewhere in the South Island, and the areas that seem to be responsible are those largely dominated by indigenous forests."
But the scientists could not rule out an important role for carbon uptake in the hill country or from pasture from current data.
In New Zealand, indigenous forests covered about 6.2 million hectares.
Scientists surprised at results
Mikaloff-Fletcher said the result was surprising one, mainly because strong carbon sinks were expected when there was a lot of forest regrowth.
"Carbon uptake this strong is usually associated with peak growth of recently planted forests and tends to slow as forests mature.
"This amount of uptake from relatively undisturbed forest land is remarkable and may be caused by processes unique to New Zealand or part of a wider global story."
The National Inventory method reported by Ministry for the Environment reports annually on New Zealand's carbon uptake.
This internationally standardised methodology puts the amount of carbon being absorbed by all New Zealand forests at 82 teragrams (Tg) CO2 (A teragram is one millon metric tonnes) total during 2011-2013, the period studied by Mikaloff-Fletcher's team.
Once accounting rule differences were corrected for, the new Niwa measurement approach found that actual carbon uptake could be up to 60 per cent higher.
The inventory-based method estimated carbon uptake using measurements of tree growth taken from about 100 sampling areas, and extrapolated this to the entire country using statistical techniques and modelling.
There was still considerable work to be done in comparing the two independent approaches.
"We need to find out definitively what processes are controlling this unexpectedly large carbon uptake, in order to understand the implications for land management and climate treaties," Mikaloff-Fletcher said.
"We need additional measurements to tell us if this is unique to the southern half of the South Island or holds across a wider range of New Zealand."
Mikaloff-Fletcher said the ability of forests to absorb carbon was a powerful tool to help address the challenge of climate change.
Next steps include incorporating data from Niwa's newest atmospheric CO2 observing site, Maunga Kakaramea/Rainbow Mountain in the central North Island, deploying two new atmospheric CO2 observing sites and a major improvement to model resolution.
This would start to shed light on what's happening in the North Island and the Canterbury plains.
The case for planting more native trees
The study comes after a major report by green business think-tank Pure Advantage last year, which called for a new national forest strategy that would halt deforestation and ultimately create 1.3m ha of new forest.
It argued that planting huge new blocks of permanent native forest and fresh high-carbon commercial forests could avoid large areas of land being lost to erosion, help off-set agricultural emissions and put the country on course for a net-zero greenhouse gas future.
Along with erosion-prone land, new forest should also be planted along waterway margins and urban forest, where the environmental benefits of trees, such as protecting river ecosystems, would be much greater.
The Government has already stated that 1.1m ha of land is erosion-prone.
Covering the entire amount in native trees would avoid hundreds of millions of dollars of lost value, while sucking at least 9m tonnes of carbon dioxide from the atmosphere every year.
New Zealand needed to expand its forest cover, prioritise forest that would remain permanent, allow for diversity in forest stocks and bolster measures to protect them, the report's author, Dr David Hall, said at the time.
It pointed to a shortage of capital as the biggest obstacle to new forest planting, but suggested ways that tree-planting could pay off, particularly by strengthening relations of responsibility between polluters and "anti-polluters".
To better incentivise planting, the report suggested that landowners should have a "smorgasbord" of funding options to pick from depending on their circumstances.
Beyond the Afforestation Grant Scheme and other Government mechanisms like the Permanent Forest Sink Initiative and Erosion Control Funding Programme, it suggested bigger and bolder measures.
On its release, the report was welcomed by the forestry industry and Associate Minister of Primary Industries, Jo Goodhew.
New Zealand and climate change
• Under present projections, the sea level around New Zealand is expected to rise between 50cm and 100cm this century, while temperatures could also increase by several degrees by 2100.
• Climate change would bring more floods (about two-thirds of Kiwis live in areas prone to flooding); make our freshwater problems worse and put more pressure on rivers and lakes; acidify our oceans; put even more species at risk and bring problems from the rest of the world.
• Climate change is also expected to result in more large storms compounding the effects of sea level rise.
• New Zealand, which reported a 23 per cent increase in greenhouse gas emissions between 1990 and 2014, has pledged to slash its greenhouse gas emissions by 30 per cent from 2005 levels and 11 per cent from 1990 levels by 2030.
