Dr Pam Rachootin raised the alarm after noticing many of her patients were refusing her offer of a free flu shot because they had already had it at their chemist.
"Of course it was the wrong vaccine, not specially formulated for flagging immune systems. I was disappointed," she wrote in industry newsletter Medical Observer.
She sent her 73-year-old husband to five chemists to see whether they would refer him to his GP for the right flu shot. None of them asked him his age or directed him to see a GP if he was over 65.
Dr Moy said the issues raised serious conflict of interest concerns about the way chemists were delivering health care.
"It certainly raises the question about whether older people are being informed they are being given the less preferred vaccine," he told News Corp.
"This is a conflict of interest issue and the management of it is different in pharmacies because they are selling something, whereas doctors don't sell stuff for monetary gain."
