The Australian Medical Association Queensland has threatened to scrap bulk-billing, saying some of its members received retrospective tax bills totalling $3 million.
The medical lobby group claims Queensland clinics are being hit with payroll tax for GPs for the first time after a recent NSW Civil and Administrative Tribunal ruling on the issue in June.
The Queensland Revenues Office (QRO) has denied changing tax assessments for clinics, suggesting recent bill increases are due to increased compliance checks.
"QRO has reviewed the NSW decision and has not identified any aspect that it considers changes the scope, practice or approach to payroll tax in Queensland," the Office told AAP in a statement on Wednesday.
"The treatment of Queensland medical practices in relation to payroll tax has not changed since 2008."
AMAQ president Maria Bolton said the tax office refused to meet to discuss payroll taxes, but the government said the QRO has met with the lobby group.
The Royal Australian College of General Practitioners said it had been assured by the tax office it had no intention of changing its existing assessments for GPs.
"The QRO has also provided us written confirmation of their position, which gives us a level of confidence that GPs won't be pursued for payroll tax," RACGP president Prof Karen Price told AAP in a statement.
"Unfortunately, we can still expect some practices to face audits, which is why we fully encourage all members, whether they are practice owners or independent contractors, to act now by seeking guidance from appropriately qualified accounting and legal advisors to review their arrangements."
Treasurer Cameron Dick said he had did not have any power over the tax assessments or collections when asked about AMAQ's claims by Opposition Leader David Crisafulli in Question Time.
"Medical practices are subject to the same payroll tax provisions in the same way that they work through the entirety of human government in which the Leader of the Opposition served," he told parliament.
"So I have consistently said in this house that the Leader of the Opposition is not a man to be trusted, and this is another example of that."
Earlier, the AMAQ president also called for GPs to be exempt from payroll tax, which it said was being considered by the NSW government.
"If NSW introduces an exemption and Queensland doesn't, our clinics will be at a competitive disadvantage and GPs will move interstate," Dr Boulton added.
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