Doctors say they have concerns about patient confidentiality after revelations the Medicare card details of Australians have been sold online, but have urged people not to opt out of a digital medical file scheme that will be implemented for all Australians next year.

Key points: Federal police investigating after Guardian journalist bought his details from "dark web"

Federal police investigating after Guardian journalist bought his details from "dark web" AMA says breach needs to be resolved so Australians do not opt out of My Health Record

AMA says breach needs to be resolved so Australians do not opt out of My Health Record Health Department spokesman says My Health Record has multiple layers of security

Federal police are investigating after a Guardian Australia journalist bought his details from a vendor on the "dark web", while Human Services Minister Alan Tudge confirmed a "small number" of details had been stolen and sold.

The Australian Medical Association is demanding answers and has questioned the Government's ability to protect patient data.

President Michael Gannon said the security breach raised concerns about digital medical file scheme My Health Record and the issue needed to be resolved so Australians felt comfortable using the system.

"It is so important, as it is with a paper record, as it is with other forms of communication that are deeply personal matters, that they are secure," he said.

My Health Record stores information such as allergies, medical conditions, treatments, and scan reports.

Almost 20 per cent of Australians have signed up to the scheme since it was launched in 2012.

A digital file will be established for every patient next year, unless they opt out of the scheme.

Fears some will opt out of My Health Record

Dr Gannon said it was important Australians used My Health Record.

"The electronic health record has the potential to reduce adverse drug reactions, to prevent allergic reactions, to reduce unnecessary duplications of investigations to save the system money," he said.

However, he said he feared many people would ditch My Health Record because of the Medicare breach.

"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.

Dr Gannon said he would raise his concerns about patient confidentiality with Mr Tudge and Health Minister Greg Hunt.

"We will be seeking reassurances that this has been looked into and that the information has been secured — that is important to us," he said.

A spokesman from the Health Department said My Health Record has multiple layers of security to protect access to the system.

"My Health Record has been in operation for over five years, with nearly 5 million Australians having a record, and in this time there have been no security breaches of patient data in the system," he said.

Medicare number theft 'traditional criminal activity'

Mr Tudge confirmed Australians' Medicare card details were being sold on the so-called dark web, but said few had actually been accessed.

"We believe that it is a small number — in the dozens — there's no indication that there's any widespread breach."

He said the matter had been referred to the Australian Federal Police and said his department was investigating the breach.

"It is not, to the best of our knowledge, a cyber incident as such, but more a traditional crime.

"I have my strong suspicions [about what occurred], but we're leaving it obviously up to the police to do a proper investigation."