Prime Minister Tony Abbott says the government will press ahead with the $7 co-payment for GP visits, but is open to discussing "practical ways" to implement it.
Australian Medical Association representatives held talks with Mr Abbott and Health Minister Peter Dutton in Canberra on Wednesday to discuss the peak body's concerns.
AMA president Brian Owler described the talks as "constructive", saying Mr Abbott had indicated a willingness to consider changes.
The AMA does not oppose the principle of a co-payment, but has been critical of the government's design.
Doctors raised concerns about charging aged-care residents, children and the chronically ill.
Mr Abbott told parliament he had made it clear to the AMA that the government was committed to a "modest price signal" for GP services, but was open to consultation.
The AMA knew that a modest co-payment would improve the Medicare system.
"That is why I am perfectly happy to work with the AMA to ensure that Australia has the best possible Medicare system," Mr Abbott said.
The prime minister later said in a statement that while the government would discuss with the AMA "practical ways to implement the co-payment" it remained committed to the policy as outlined in the May budget.
Labor and the Greens are opposed to the co-payment and the government will need to talk to the new Senate crossbench to approve its legislation.
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