BHP Billiton, Rio Tinto and Xstrata have called a meeting to consider abandoning their tax deal with the PM.
It comes after the federal government admitted it was seeking to back away from a key part of the deal.
The dispute also centres on whether miners or the government are exposed to a potential multi-billion-dollar bill for increases to state mining royalties.
Earlier this year BHP and Rio Tinto agreed to pay an extra $1 billion in iron ore royalties to Western Australia over the next four years, but there is now doubt over whether this will be returned to miners under the planned tax.
BHP Billiton has done little to douse speculation it's ready to walk away from a resource tax compromise deal with the government.
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Liberal senator George Brandis said this was a "very grave" situation. The coalition has opposed a mining tax since it was first announced on May 2 as part of the government's response to the Henry Tax Review.
"Three of the biggest companies in the world thought they had a deal," he said, while quizzing Resources Minister Martin Ferguson's department during Senate budget estimates hearing on Wednesday.
Under the original resource super profits tax (RSPT) announced by the then Rudd government, state royalties would be refunded as they stood on May 2, 2010, but the heads of agreement with BHP Billiton, Rio Tinto and Xstrata for the MRRT imposed no such limitation.
"That question will be one addressed by the policy transition group ... and a decision will be made in due course," the secretary of the Department of Resources, Energy and Tourism Drew Clarke told the hearing. The policy transition group is headed by Mr Ferguson and former BHP chairman Don Argus.
Senator Brandis said it was one thing to have this group to consult on implementation issues, but quite a different matter to consider it was not bound by the terms of the heads of agreement.
Senator Nick Sherry, representing Mr Ferguson at the hearing, said the government was not walking away from the agreement.
"It is appropriate for the policy transition group to discuss these issues," Senator Sherry said.
"Where there has been a different view, as there is ... it will be the task of the policy transition group to consult on this matter."
The hearing was also told that the department was not aware of advice obtained from the Australian government's solicitor by Treasury over the legality of the original RSPT until it appeared in the West Australian newspaper.
The advice raised serious questions as to whether the original RSPT was constitutionally valid because of the different state royalty regimes and was more serious if the level of the tax offset claimable was fixed on a certain date, Senator Brandis said.
The policy transition group has had one formal meeting - on September 20 - and has held a series of consultation meetings since in Perth and Queensland over four days, as well as interim phone calls.
"We now know those consultations were held in ignorance of this advice," Senator Brandis said.
Ms Gillard told reporters in Canberra the government had said all along that it would credit "existing royalties and scheduled increases".
"In implementing the mineral resources rent tax we, obviously, won't be giving a green light to state and territory governments to increase their royalties in a way which means the federal government effectively foots the bill," she said.
