"However, there is no current or foreseeable methodology that will provide an accurate measure of greenhouse gas emissions on an individual farm, nor of what any particular mitigation measure might achieve at a farm level."
Currently, at an individual farm level, emissions could only be estimated through proxy measures using scientific models such as OVERSEER, which, the sector argued, wasn't good enough to use as a blanket regulatory tool.
But Sir Peter said one potentially feasible option could be a "farm plan approach" where a farmer, backed by science and expert advice, could identify their own strategies to lower emissions.
Such schemes could begin as voluntary initiatives, but ultimately would require policy and action to get results across the sector.
"Compliance or otherwise with an appropriate farm plan could extend to other dimensions of environmental management and to animal welfare and could be linked to any market or regulatory incentive scheme," Sir Peter said.
"Such an approach would require greater focus on the skillset of appropriately accredited farm advisers."
There was a risk that, without such oversight, farmers could find themselves cutting emissions in one area at the expense of increasing them elsewhere.
In the longer term, there were compelling reasons to keep pushing for science breakthroughs, such as new compounds that could slash the amount of methane an animal produced.
"It is clear that, apart from substantial land-use change and afforestation, the main opportunities to reduce emissions significantly will depend on technological innovation such as the use of inhibitors."
The report comes soon after one of the scientists leading that work, Dr Andy Reisinger, laid out some figures around the gains that farmers would need to make in cutting methane.
To ensure methane from livestock contributed no additional warming beyond current levels, emissions would need to be cut by at least 10 to 22 per cent below 2016 levels by 2050 - with further reductions of between 20 and 27 per cent by 2100.
Reisinger also reported how holding livestock methane at present levels wasn't an option, as doing nothing would cause additional warming of 10 to 20 per cent above current levels.
Last week, the Productivity Commission recommended that animal-made methane should be accounted for within either a dual-cap Emissions Trading Scheme (ETS), or some alternative quota system.
Under the ETS, the commission said, the Government could also set a "farm-level" threshold for emissions not caused by the use of fertilisers - and make manufacturers and importers accountable in the ETS for fertiliser-sourced nitrous oxide emissions.
While among the biggest contributors of greenhouse gases in New Zealand, the agriculture sector has opposed being pulled into the ETS, arguing that our trading partners didn't force the same rules on their farmers, and, again, that there wasn't an accurate way to measure and report farm emissions.
The Government has yet to decide how - or whether - shorter-lived gases are dealt with by the Zero Carbon Bill it's soon to introduce.
Nonetheless, Sir Peter said that arguments for focusing on carbon dioxide and nitrous oxide and giving less emphasis to methane were "counter-productive" - and his new report didn't favour avoiding a focus on it.
"It is unrealistic, however, to imagine that we can get to a greenhouse gas-neutral profile from agriculture without offsets in various forms," he said.
"Despite the many scientific, economic and implementation challenges, failure to take action in the agricultural sector will not only be costly to those farmers who find themselves unprepared for change, it will also ultimately be costly to New Zealand."
