The AMA recently wrote to the Queensland government's chief health officer calling for the matter to be addressed as a priority.
"Pharmacies have no proven record that they are safe or appropriate locations for such a private and potentially risky clinical procedure as vaccination," said AMA President Dr Steve Hambleton.
"Vaccination saves lives and improves quality of life for millions of Australians and should be performed by appropriately trained and accredited health professionals, doctors, or under direct supervision of doctors in a safe and private clinical environment.
"The AMA believes that general practice is the appropriate location for vaccination, with the procedure conducted by a highly-trained and accredited GP or by an appropriately trained and qualified general practice nurse under the supervision of a GP.
"Pharmacists provide the community with a highly valued service — as pharmacists. They should not pretend to be doctors."
Dr Hambleton said that all medicines carry benefits and risks.
"Health practitioners who perform vaccinations must have specific training that includes how to make an assessment about the safety of the vaccine for a particular patient, and how to recognise and respond to adverse reactions," he said.
"It is not in the interests of patient safety for pharmacists to participate in this irresponsible trial; it could even be dangerous.
"There are issues with privacy, training, accreditation, qualifications, side effects, patients' medical history, consistency of medical records, sterilisation of equipment, appropriate storage of vaccines, and professional indemnity, to name just a few.
"Is there a loading on the professional indemnity insurance for pharmacists who wish to participate in the trial?
"Where is the private area to seek consent?
"Where is the private bed to assist patients who wish to lie down?
"Where is the private area where patients can wait after vaccination until it is confirmed that there is no immediate allergic reaction?
"Where is the private area where a resuscitation can occur if needed, until the ambulance arrives?
"How do we prevent duplication of vaccination if there it is not an established routine to either seek information from the patient's usual doctor or to inform the usual doctor?
"The safest way for people to receive vaccinations, whether for flu or to prevent other conditions, is through their usual general practice.
"Vaccinations outside general practice must be subject to the same proficiency and quality requirements as those provided within a general practice.
Dr Hambleton asserted: "The Queensland trial does not meet these requirements and must cease immediately."