Critics warn it could put your most sensitive information in the wrong hands.
Advocates say it will save lives, particularly those of people living in rural and remote areas.
Beginning now, ((mon)) everyone is automatically signed up to a system known as My Health Records, but there is a three-month window to opt out, or have your records removed, from the electronic database.
The Australian Privacy Foundation’s Bernard Robertson-Dunn advocates opting out.
"I would say, ‘Opt out now.’ You always have the option of opting in later when you can make a more informed decision."
But the Digital Health Alliance’s Professor Meredith Makeham says she disagrees.
"As a GP, I really encourage my patients to have a My Health Record, because I believe it offers people a range of really important benefits -- and, particularly, around safer care and better health outcomes."
The system has been in operation for six years, but people have had the choice of opting in if they chose to do so.
And almost 6 million people have.
But now, with opting in an automatic decision unless otherwise requested, privacy experts have expressed particular concern, about cybersecurity and about the government having access to such sensitive information.
"The government doesn't own it. It’s the custodian of the data. But the government has complete control over it. That means that, if you want to delete the data, the government won't (do it). They will hide it, but they will not delete it.”
The agency rolling out the program says the idea is to put patients in control.
People can access their own information and be notified when someone has looked at their data.
The agency insists the system has military-grade security and has not suffered a breach in the six years so far.
Professor Makeham says the company is taking all the necessary steps to ensure privacy standards.
"There is no complacency here. We constantly surveil and threat-test the system, and it operates at defence-level standards."
Health Minister Greg Hunt says he is confident in the system.
"It's arguably the world's leading and most secure medical-information system at any national level. It has been operating for six years with almost 6 million Australians without a breach."
And National Rural Health Alliance chief executive Mark Diamond says people in regional areas will benefit the most from having medical information readily available to doctors.
"What the My Health Records enables is them to be able to access your personal health information immediately in life-threatening situations."
Patients seeking more information are encouraged to go to the My Health Records website.
The chance to opt out closes on October the 15th.
