Forest & Bird have pulled out of the Land and Water Forum in protest against the government's new "timid" freshwater standards.
The forum gives more than 50 stakeholders, including industry groups, non-governmental organisatins (NGOs), iwi, scientists and others a chance agree on recommendations to be made to government.
However, Forest & Bird said those recommendations had been largely ignored in the government's plan to make 90 percent of rivers swimmable by 2040.
Forest & Bird said the recommendations had buy-in from all the relevant stakeholders and incorporated the best scientific advice, but what the government had come up with was very different.
The government announced last month a goal to make more rivers swimmable but it would do so by weakening the threshold for what qualifies as the best quality waterway to swim in. The move has been criticised by some scientists and environmentalists.
The Land and Water forum has existed for nine years, although Fish and Game withdrew from it in 2015, saying it was being muzzled and stopped from speaking out on environmental issues.
Forest & Bird said the government's swimmable water move had undermined the good faith and trust extended to the forum to help address the freshwater crisis.
The NGO's chief executive Kevin Hague said the government's announcement did not go nearly far enough.
He said the New Zealand public were very concerned about freshwater quality, and that scientists had been saying the ecological health of the country's waterways was severely at threat.
"This very timid gesture by the government in the face of actually some pretty good consensus recommendations from the Land and Water Forum really says there's nothing to be gained for Forest and Bird to stay in this process," he said.