The Government intends on reintroducing its Carbon Pollution Reduction Scheme - for the third time - to Parliament in May and while agriculture is excluded, there is still concern about what impact the scheme might have on indirect costs like fuel, freight, fertiliser and electricity.

Mr Burke told last week's ABARE conference in Canberra that with agriculture out of the Government's scheme and assistance for fuel costs and conversion to low-energy use in the processing sector, the cost impact on farm inputs would be "neutral".

But NFF emissions trading spokesman, Charlie McElhone, said Mr Burke's advice is contrary to what NFF had calculated and provided to the minister.

Mr McElhone said it was already very clear that even though agriculture will be excluded under the Government's ETS and there would be some short-term assistance in the area of fuel, costs would still be incurred for inputs which remained a big concern for farmers.

"Claims the cost impact on inputs will be neutral is just not the case," Mr McElhone said.

"Energy and energy related costs can make up to 45 per cent of input costs for grain farmers.

"The Government has announced a fuel rebate scheme for the first three years of the scheme which will offset some of those costs but there are no guarantees after those three years.

"In fertiliser, those costs will most certainly go up, and there will be impacts for machinery and freight, so neutral is not how we would describe those impacts at all."

Mr McElhone said rising input and indirect costs on farmers as a result of the emissions trading scheme was the biggest concern to farmers about its introduction.

Mr Burke last week said the Government had done a "terrible job" explaining the carbon pollution reduction scheme and Mr McElhone agreed a major education campaign was still needed to explain the details of the policy to farmers.