Climate Change Minister James Shaw said the report was based on the "best science and economic advice there is".
"On balance I think they have landed in the right place."
It would still need to be considered by Cabinet, and they would be seeking bipartisan support - as with the Zero Carbon Act - to ensure it was enduring.
National Party climate change spokesperson Stuart Shaw said it was "no question" his party supported reaching net carbon zero by 2050, as set out in the Zero Carbon Act.
He reaffirmed his party's support for the Commission and its "carbon budgets" to reach the goal, and said it was National that signed New Zealand up to the Paris Agreement in the first place.
However, he said he was concerned at the "policy interventions" designed to reach those goals such as "feebates" to promote electric vehicle uptake.
Instead, he said the emissions trading scheme (ETS) needed to be better utilised to allow the free market to drive innovation.
"The ETS is the mechanism to lower our emissions and if a is policy proposed instead, we need to know why, know the costs and benefits of that and why the ETS can't achieve that."
Farmers were also being asked to do more than originally proposed, he said.
Also of concern was the first emissions budget, which had New Zealand reducing emissions by 8 per cent in just four years, between 2022 and 2025.
"Given that, under this Government, emissions have increased by 2 per cent and we're on track to burn over two million tonnes of coal this year generating electricity, we first have to slow down our emissions to bring them back to zero before we start reducing them.
"So it's quite a challenge. However, as the Government reflects on and works through this report, we will continue to advocate for New Zealanders to ensure that we are not having command-and-control policies foisted upon us."
Act leader David Seymour said New Zealand needed to play its part on climate change, but questioned why it was trying to "lead the world" given its small footprint.
"If the rest of the world wants to decarbonise, then we should track them. It is dangerous for a small trading nation to get out of sync with its trading partners for reasons of diplomacy, trade and consumer preferences.
"It would be foolish for New Zealand to 'lead' the world. Whether we like it or not we are a passenger on this journey, our emissions alone will not change the climate."
He also said having an ETS with a carbon cap ran counter to the goals of policy interventions.
"The Government shouldn't micromanage the economy to reduce emissions. It needs to set the cap on carbon credits in line with other, similar countries' emissions."
Te Paati Māori co-leader Debbie Ngarewa-Packer said they welcomed the report, especially given tangata whenua had the "most to lose" from climate change, along with Pasifika whanaunga facing the prospect of losing their Islands due to sea-level rise.
Environmental protection and restoration could not be achieved without acknowledging and implementing Māori rights and recognising the role of tangata whenua as kaitiaki, Ngarewa-Packer said.
"That includes actually returning our land and our resources. We cannot beat the climate crisis without restoring lands to their rightful indigenous owners, who know how to manage that land in harmony with the climate."
She called for fewer cows, and for onshore oil and gas permits to end, and both existing onshore and offshore permits to be withdrawn, with the target of decommissioning all sites by 2030.
Māori and equity issues
One of the key changes from the draft report released in January was an increased focus on partnerships with iwi and upholding Te Tiriti o Waitangi.
In response to "significant feedback", the commission said:
"The transition to a low emissions society in Aotearoa must be equitable for tangata whenua and all New Zealanders.
"To achieve this, the impacts of the transition on Iwi/Māori need to be understood from a te ao Māori view."
Māori, as with indigenous groups worldwide, are among the most vulnerable groups to climate-change impacts due to their "significant reliance on the environment as a cultural, social and economic resource".
The Māori economy relied heavily on primary industries, and many communities were near the coast. Already many urupā (burial grounds) and marae were being flooded or washed into the sea.
There were also equity issues, given those with higher levels of poverty and socioeconomic inequality were going to be less able to adapt easily to new policies and impacts of climate change.
The commission also called for proactive partnership with iwi/Māori and to advance a Māori-led approach to an equitable transition for iwi/Māori.
Māori Climate Commissioner Donna Awatere Huata said Māori were ready to be involved in partnership and "active contributor".
"It is no longer good enough to have to have a conversation, for the Government and its officials to seek consultation or use policy frameworks to assess impact on Māoridom.
"Māoridom stands ready to walk alongside the Government, to take the steps required to assist the transition to a low carbon economy.
"But to do this, Māori must have a say over how their contributions are used and how the settings that unlock their contributions are framed."
E tū union also welcomed the report, and its policy directions for a "fair, inclusive, and equitable transition for workers and their communities", researcher Sam Huggard said.
Job losses, such as more than 2000 mechanics and farm workers by 2035 due to industry changes, were predicted as the economy decarbonised.
However, new jobs would be created in a range of clean energy and new technology industries.
Huggard said the advice covered proactive transition planning with all parties at the table, widely accessible education and training, dedicated support for workers in transition, and better analysing the distributional impacts of climate policies on population groups.
"Workers know that change is coming to their jobs as a result of climate change and other trends, such as automation — that's why a just transition is so necessary."
However, significant investment needed to develop new industries or support existing ones to transition to a low-carbon future, he said.
Industry cautiously welcome report
Paul Goodeve, chief executive of gas network Firstgas Group, said they welcomed the commission's shift from bans on energy sources to transition to low-emission alternatives.
"The [commission's] final advice is more supportive of preserving our ability to decarbonise multiple energy distribution channels, including using zero carbon gases like biogas, bioLPG and hydrogen," Goodeve said.
"The commission has removed the draft ban on new gas connections, and an initial recommendation to replace gas appliances with electric alternatives.
"This means gas users can work towards our national target of zero emissions without resorting to electrification or carbon offsets, and without the need to replace their current gas equipment."
The final report recommends Government sets a target for 50 per cent of all energy consumed comes from renewable sources by the end of 2035; supports the development of bioenergy and hydrogen; and evaluates the role of biogas and hydrogen as an alternative use of pipeline infrastructure.
Federated Farmers president Andrew Hoggard said proposed cuts to livestock of as much as 15 per cent by 2030 was "probably doable", provided various technologies eventuated and land-change trends continued with farms being converted into urban areas, forestry and horticulture.
"The key is it could happen anyway, I'd be more happy if the market drives it, if farmers choose to do this."
Hoggard said they were worried about unintended consequences of too much pressure on agriculture, as New Zealand was already one of the best producers of food at a low carbon rate.
"We don't want to have to slash production here only to shift offshore at higher emissions."
