A trial proposed for North Queensland would allow pharmacists to prescribe medicine for serious conditions and chronic illnesses, AMA Queensland says.
The 23 conditions include asthma, type 2 diabetes, heart failure and middle ear infections, and it would mean patients could access medicine without a GP consultation.
It has been proposed for 37 local government areas in North Queensland which have "significant indigenous populations and serious doctor shortages", the AMA says.
Speaking ahead of a state parliamentary inquiry on Friday, President Chris Perry says medical association members "overwhelmingly" oppose the proposed pilot.
""It's fundamentally flawed and will deliver second rate health care to people in North Queensland," Professor Perry said.
While pharmacists are a vital part of health care, they do not have the training to diagnose serious health conditions, AMA Queensland Council of General Practice Chair Maria Boulton.
"GPs on average have 12 years of training under their belts before they start diagnosing and treating these conditions," she says.
Dr Boulton is expected to speak at Friday's wide-ranging inquiry into the public health system.
The AMA has written to the Therapeutic Goods Administration seeking advice on the trial's potential impact on Australia's health system.
"For example, the trial will allow pharmacists to prescribe the oral contraceptive pill - a move expressly outlawed by the TGA late last year given the health risks for patients," Prof Perry said.
"We are seriously concerned that this trial will lead to significant misdiagnosis of potentially serious conditions plus undermine attempts to manage antimicrobial resistance."
The AMA initially agreed to take part in a steering committee for the pilot, but now says it fundamentally rejects the proposal.
The National Council of Primary Care Doctors has also written to Queensland and Federal health ministers recommending that the pilot be stopped.
Queensland Health has been contacted for comment.
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