THE two "heavies" of rural politics - the Nationals and the National Farmers' Federation - have gone toe to toe on emissions trading.

Nationals Senate leader Barnaby Joyce has ripped into the NFF for backing pro-farmer amendments to the Federal Government's Carbon Pollution Reduction Scheme.

But NFF boss David Crombie has hit back, saying the NFF's job was to protect farmers' interests and dismissing the criticism as "not important".

The rising tensions have come in the wake of coalition plans to amend the CPRS to exclude farmers, provide them with carbon offsets and better protect food processors.

Senator Joyce said no matter how the CPRS was changed, it was still just a "massive tax", which would hurt rural Australia.

"The NFF is supposed to represent farmers but I can't find any farmers that support an emissions trading scheme," he said.

"I think their members will be bitterly disappointed with where the NFF's position is going to leave them.

"The last time I got advice on how to vote from the NFF, it was to sell Telstra."

Mr Crombie said the criticism was "unfortunate but not important".

"If Australia is to have a CPRS, then it is our job to make sure farmers' interests are protected.

"My only concern is dealing with the legislation and protecting the interests of agriculture.

"I will leave it to others to understand why the NFF is being criticised by a coalition partner for supporting coalition amendments to the CPRS."