Doctors will be seeking reassurances from the federal government that patient records are secure as authorities investigate a possible breach.
Federal Police are looking into a Guardian report in which one of its own reporters was able to buy his Medicare card number from a "darknet" trader for less than $30.
Human Services Minister Alan Tudge has stressed no one's health records can be obtained with a Medicare number.
But the Australian Medical Association wants answers as to how this was able to occur.
"This is a deeply concerning development," president Michael Gannon told ABC radio on Wednesday.
But he hopes Australians don't opt out of the electronic My Health Record, which aims to reduce adverse drug reactions and prevent allergic reactions.
"It is so important for the success of the My Health Record that doctors and patients both have absolute confidence in the integrity of the system," Dr Gannon said.
