Queensland GPs working as contractors at clinics won't be getting a payroll tax exemption, the state treasurer says.
The Australian Medical Association Queensland (AMAQ) threatened to scrap bulk billing on Wednesday, saying some of its members had received retrospective tax bills totalling $3 million.
AMAQ president Maria Boulton accused authorities of charging general practices payroll tax for GPs.
Treasurer Cameron Dick says tax arrangements haven't changed, but compliance checks have ramped up since the COVID-19 pandemic's peak.
He says only four of the 71 businesses found to have compliance issues since July are medical practices.
"That's because they're contractors, not because they're GPs, and not because GPs are being specifically targeted," Mr Dick told reporters on Wednesday.
"As is the case with income tax, compliance issues may be identified in previous years, that's the same for any taxpayer.
"But when they're identified businesses that owe payroll tax, you can ask the revenue office for a repayment plan if they need to catch up on their obligations."
Ms Boulton has called for GPs to be exempted from payroll tax, an arrangement she said was under consideration in NSW.
Mr Dick has ruled that out, saying all businesses should pay the correct tax as economic conditions return to normal.
"We helped them get through COVID through payroll tax refunds, deferrals and holidays, but as our economies are strengthening again we need to get back to where we were, which is regular compliance activities - nothing more or nothing less than we did prior to COVID - to make sure everyone pays their fair share of tax revenue," he said.
Earlier on Wednesday, the AMAQ claimed GP taxes had changed following a NSW Civil and Administrative Tribunal ruling on the issue in June.
The Queensland Revenue Office (QRO) denied the NSW decision had changed the scope, practice or approach of its tax collection.
"The treatment of Queensland medical practices in relation to payroll tax has not changed since 2008," the department told AAP in a statement.
Ms Bolton also said the government refused to meet her group for talks, but Mr Dick said the revenue office met with the AMAQ and the Royal Australian College of General Practitioners (RACGP) last month.
RACGP president Karen Price said the tax officials had stressed they had no intention of tax changes for GPs.
"The QRO has also provided us written confirmation of their position," Professor 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."
