Federated Farmers is urging the government to be less political and more transparent in its approach to climate change.
This has come after criticism the Zero Carbon Bill was introduced to parliament before a report by the Interim Climate Change Committee was revealed.
That report was intended to contain practical recommendations on how farmers could reduce their emissions.
Then Zero Carbon bill was introduced to parliament on 8 May.
The report by the Interim Climate Change Committee only came out 17 July.
That left farming organisations scrambling to address two overlapping issues at the same time.
Minister for Climate Change James Shaw was asked last week about this apparent confusion by a member of the Youth Lobby Group, Generation Zero.
"I think your question implies a level of joined-up government that doesn't actually exist," Mr Shaw said.
"That is actually a coincidence rather than design."
Mr Shaw was then asked why the report by the Interim Climate Change Committee was withheld from the public for about a month.
"We've had as a government some experience recently where we have released independent reports without our response.
"That has created something of a vacuum [for the National Party] to project their howling demons and create a level of opposition that is not founded in fact."
Mr Shaw said it was better to release the report and the government's response at the same time.
But Federated Farmers' climate change spokesman Chris Lewis said this was not good enough.
"It's a bit disappointing that Federation Farmers has to make a strong submission on behalf of its members before it has all the evidence in front of it."
The director of the Institute of Public Administration of New Zealand (IPANZ), the public sector watchdog, described the government's handling of this as "kind of messy".
"But the world is never perfect and you do your best with the hand you have been dealt."