The Kimberly Land Council (KLC) chief executive Nolan Hunter said the repeal is a major blow to the region's communities.
He said it will stop Indigenous people in the region from participating in the carbon economy.
"This is a major smack in the face," Mr Hunter said.
Currently, Indigenous organisations sell carbon credits through the Carbon Farming Initiative (CFI) – the Council says the initiative has already earned Traditional Owners 230,000 credits – worth $5.3 million.
Under the CFI, farmers and landholders can earn credits by taking steps to reduce greenhouse gas emissions thus earning carbon credits they can then sell to other organisations.
Mr Hunter said the introduction of the CFI was a new way for traditional owners to generate income in areas where there was little to no industry.
"People saw that as a way to create opportunities, income, business opportunities and employment and training opportunities and a whole range of opportunities that would come from being able to generate income to do things further in their community to develop their community," he said.
He said the federal government’s proposed replacement for the carbon tax, the Emissions Reduction Fund, would force Indigenous farmers out of the carbon industry.
The government, howevever, says the proposed fund is key to balancing environmental concerns and business competitiveness.
It says carbon taxes put too much of a cost burden on households and businesses.
The Reduction Fund looks to sell carbon credits in a reverse auction – this means the credits will be sold at the cheapest price.
"Small groups like us won’t be able to compete to be able to lower the price of carbon credits," Mr Hunter said.
"Those bigger companies – the economy of scale issue is that they can afford to drop the price to a sustainable level whereas small businesses that we’re trying to create will be knocked out of that."
Mr Hunter and the Kimberly Land Council are calling on the Senate to make an informed decision when voting on changes to carbon legislation.
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