Prime Minister Tony Abbott is standing firm on introducing a fee for visits to the doctor, but he has given his clearest signal yet that a compromise deal could see pensioners face a lower GP co-payment.

As the government negotiates with the crossbench, Mr Abbott said he expected the $7 payment would eventually pass the Parliament, despite stiff opposition from the Palmer United Party to the measure in its current form.

Mr Abbott has refused to explicitly say what ground the government could give on the $7 fee policy, but hinted broadly at the direction the government was considering.

"We don't exempt pensioners from a PBS [Phamraceutical Benefits Scheme] co-payment," he told Brisbane radio.

"Their co-payment is normally a little less than the co-payment that the public faces.

"So if we don't exempt pensioners from the PBS co-payment, why should they be entirely exempted from the Medicare co-payment?"

The Prime Minister’s comments came as the government appeared to be attempting shift the budget narrative away from one of “crisis” - Finance Minister Mathias Cormann said on Monday night negotiations would be a “marathon, not a sprint” – and as the government released modelling that showed only about $20 billion of $19 trillion of expenses over four years contained in the budget had not been passed.

The government is now stressing that the current political debate about the budget is about structural measures that for the most part will not come into full effect until the fourth year of the current budget, with savings to ramp up over the next decade.

About $40 billion in savings have not been passed when other measures, such mining tax-related expenditure, are included.

Mr Abbott said the GP fee was one measure that he believed the government would win approval for because it "makes sense".

"I'm pretty sure that we will end up with a modest co-payment," Mr Abbott said.

"The precise detail of the arrangement – let's wait and see how we go with our discussions ... with the crossbench.''

He said a fee "makes economic sense, it makes health policy sense".

"Frankly, it makes fairness sense," Mr Abbott said.

"Because in the end these systems have got to be sustainable."

Treasurer Joe Hockey also defended the proposed fee, saying directing the capital in the medical research fund would help the budget bottom line.

''Effectively the savings in health go into the medical research future fund. And given that all that money is not going to be spent, but the return on the investment from the medical research future fund will gradually increase over time, the overall benefit of our health reforms is a significant saving to the budget,'' he said.

Asked why the government had not made that argument before, Mr Hockey replied: ''We have, but perhaps you didn't hear it.''

Shadow treasurer Chris Bowen said on Wednesday the government could not argue that the medical research fund, which its co-payment was intended to fund, was part of its budget repair strategy.

Mr Bowen said the proposed fee was simply "a matter of prejudice and it’s a matter of undermining the fundamental universality of health care".

"It is charging people to go to the doctor which means your wealth will determine your health.

"That is completely undermining the principles of Medicare which have existed now in Australia for 30 years, were bipartisan, it's in clear breach of an election commitment and we won’t stand for it."

Mr Abbott's comments come after Finance Minister Mathias Cormann moved to reset the budget debate overnight, calling for a "reality check" about the state of the Australian economy.

Senator Cormann rejected media discussion of the budget as "noise" and said suggestions the budget was unfair were "nonsense".

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