Atlas Iron says it doesn't expect to pay any mining tax and the Federal Government will not make as much money as it expects from the new policy.
The Australian reports Atlas Iron managing director Ken Brinsden said the company had almost finished its analysis of the tax and it was not expecting to be liable.
"Clearly, we don't expect to be paying MRRT in the foreseeable future barring a material change in the iron ore market, therefore, the Government won't be getting the revenue that it expected," he said.
According to The Australian Brinsden said because Atlas didn't expect to pay the mining tax there was a "good chance" that most other companies wouldn't either.
After launching a High Court challenge against the mining tax last month Fortescue Metals Group director of operations Jamie Frankcombe said FMG also expected the cost of the mining tax would be negligible.
"We haven't changed our views that our payments in relation to this tax will be negligible in the next few years and we think all other mining companies are in the same boat," he said.
The claims by Atlas and FMG over their liability contradict previous claims by the companies and highlight the confusion still plaguing the industry.
FMG previously argued that Rio Tinto, BHP, and Xstrata secured a favourable deal from the Government over the mining tax that would push most its burden on to smaller companies.
The Minerals Council has previously claimed there was no discrimination in the tax, and the MRRT even had provisions "designed to lower the overall burden of the tax on smaller miners".
Some analysts have also claimed the coal industry will pay little under the tax, but the Gillard Government says it expects to make almost $10 billion in the first three years of the policy.