Prime Minister Tony Abbott has denied he made a "captain's call" on the proposed cut to the Medicare rebate for short GP consultations, but he says there was a "vigorous" discussion within Cabinet about the policy.

The proposed $20 cut to the rebate for consultations under 10 minutes was due to come into effect on Monday.

But Health Minister Sussan Ley announced last week that it would be taken off the table in the face of a sustained campaign by doctors and the Government's political opponents.

The ABC has confirmed Treasurer Joe Hockey and the health minister at the time, Peter Dutton, were opposed to the rebate cut when it was first announced in December as part of the Government's revised GP co-payment policy, but were overruled by the Prime Minister.

"As you'd expect, there are lots of vigorous discussions inside the Cabinet, inside the national security committee, inside the expenditure review committee, but all decisions are unanimous and this certainly was a unanimous decision," Mr Abbott told reporters in Sydney.

He added it was "not true" to suggest that he had a heated argument with Mr Hockey and Mr Dutton.

Mr Dutton used a Tuesday night appearance on the ABC's 7.30 program to defend Mr Abbott's leadership.

"I think people see in Tony Abbott a very strong leader and we will continue to prosecute the message that we want to get our country back on track and I think Tony Abbott's doing a very good job," he said.

The Prime Minister said the Federal Government was still committed to making changes to Medicare to make it more sustainable, including "more price signals over time" for those who can afford to pay more.

But he said shelving the short consultation rebate cut was the sensible option.

"We've done what needs to be done. We've taken this particular element of a series of proposals off the table, pending further consultation with the medical profession," he said.

"If you propose something, if you find that it's causing a problem, you take it off the table – you consult and you fix it.

"And that's exactly what we'll be doing."

Higher education on the agenda when Parliament returns

The future of Medicare is just one policy to be negotiated with the Senate's crossbench this year.

Mr Abbott has confirmed the planned changes to the higher education system — which are also still to make it through the Senate — will lead the Government's agenda when Parliament returns next month.

"It's very important for our universities. It's very important for our future as a creative, dynamic society and economy, and that's why we are absolutely persisting with these important reforms," Mr Abbott said.

But Greens leader Christine Milne said her party would not shift from its opposition to the package.

"The Greens won't be compromising on deregulating university fees. We don't believe it's a good idea," Senator Milne said.

"We want to see as many people as possible go to university and have access to the courses they want to complete."

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Deputy Opposition Leader Tanya Plibersek said the Government cannot blame Labor for refusing to support its plans.

"What the Government's saying is that you've got a generation of students being held to ransom — if Labor doesn't do something then this generation of students will suffer," she said.

"It's actually up the Government to come up with a solution that shows that we value higher education."