Nearly every general practice is expected to sign up to the Government's new zero fees for under-13s regime, though some say they cannot rule out raising the cost of adult consultations to cover their costs.
The policy was widely praised by health professionals, though doctors said its true value would not be apparent until the level of state subsidy was confirmed.
The Rural General Practice Network, which represents 200 rural GP clinics, said incomes at these practices took a hit when free visits and prescriptions were introduced for children under 6 because funding did not completely cover the cost of the appointments.
Chairman Dr Jo Scott-Jones said: "We're really enthusiastic about the idea of providing care that's free at the point of contact, it makes a lot of sense. But it needs to be done in a way that's sustainable for the businesses."
Private clinics will be able to opt out of the new $90 million policy if they feel that it will not pay off.
Just 2 per cent of 1029 clinics opt out of the current scheme for under-6s, and Health Minister Tony Ryall is expecting a similar participation rate for the expanded regime.
GPs said yesterday that it was difficult to confirm how many clinics would choose to participate until they knew how much they would be subsidised per patient.
Medical Association head Mark Peterson said making doctors' visits fully funded led to not only more patients, but more frequent visits.
"There's evidence in the UK, where consultations are free for everybody, that consultation rates are higher there than they are here. In other words, the patients go more often per year than they do here."
He said this could lead to GPs increasing consultation rates in order to cross-subsidise the cost of seeing more children.
"In which case, we might go back to the Government and say when we did the maths initially it was based on the average child consulting twice a year, and now they consult three times a year, we're actually 50 per cent worse off."
At present, clinics received an average of $74 per enrolled child to provide free visits for under-6s.
Dr Peterson said that this rate of subsidy typically meant that practices made a loss on the zero fees scheme and made up the money elsewhere.
The introduction of the new policy has been scheduled for July 2015 to give time for the Ministry of Health to consult GPs over the level of subsidies.
A ministry spokesman said it was important to note that under-6s went to the doctor considerably more often than children aged between 6 and 12.