Deputy Prime Minister Grant Robertson said he understood the "pressure" rural communities felt under the weight of Government policy reforms, but he urged protesters to be "respectful".
His comments came in the midst of the Groundswell movement organising protests in towns and cities throughout the country, which included a convoy of tractors parading down Auckland's Queen St.
The Howl of a Protest event was organised against policies like the Clean Car Discount, which will subsidise clean vehicles by charging fees on high-emissions vehicles. Protesters were also anxious about the eventual pricing of agricultural emissions, which will happen by 2025 - a decade after agriculture was first slated to enter the Emissions Trading Scheme.
Robertson said he understood the pressure of change could be challenging.
"There are a lot of things happening at the moment in the economy to try and make sure New Zealand's economy remains both fiscally and environmentally sustainable - we've been working very closely with rural communities on this," Robertson said.
"I understand that at the farm level they are feeling the pressure of that change," he said.
Some of the signs at the protest contained offensive slurs - Robertson said he had seen "one or two signs" that did not fit his definition of respectful, but would not say which ones they were.
"Every New Zealander has got a right to protest and a right to put their views forward, but I always think it's important in these situations to be respectful," Robertson said.
He urged farmers to work with the Government.
"What I'd say is we have to work together on that, just as we worked together to resolve issues around Mycoplasma Bovis, just as we worked together to support those who lived in rural communities through Covid, just as we worked together to ensure air freight gets out and exports get out," Robertson said.
He echoed comments made by Prime Minister Jacinda Ardern earlier this week that action on climate change was important for New Zealand's trading relationships.
"Climate change is one of the examples where we have to work together with the rural sector.
"We rely on a stable climate, we rely on a clean green image for the prices that we get overseas," Robertson said.
The protest has whipped up a political storm in Parliament with nearly every National MP deployed to a protest site around the country. The party launched a new ad against the Clean Car Discount to coincide with the protest.
Calling the discount policy a "ute tax", National leader Judith Collins said it "unfairly penalised farmers, tradies and others who rely upon vehicles for which there is no electric alternative".
"Farmers helped New Zealand get through the Covid-19 lockdown and today their protests around the country demonstrate how out of touch the Government is with rural New Zealand," she said.