The three month opt-out period has begun for the My Health Record database amid digital security and privacy concerns.

Australia's electronic health record system has military-grade security and people should stick with it, Health Minister Greg Hunt says.

Almost six million people have signed up for a My Health Record - a digital medical history - over its six years of operations.

But there are fresh concerns of possible cyber-security threats and privacy breaches.

The government has opened a three-month opt-out window, ending on October 15, for people who do not want a record created for them.

After this date an e-health record will be created for every Australia by default.

A number of people reported on Monday not being able to log in or get through to a hotline to opt out of the scheme, but the problems were being ironed out.

Mr Hunt said world-leading security had meant there been no breaches of the system over the past six years.

"It is not just bank-level security but the advice from the Digital Health Agency is that it has been defence-tested," Mr Hunt told reporters in Melbourne on Monday.

"They have a permanent cyber security network. It's arguably the world's leading and most secure medical information system at any national level."

As well, every Australian personally controlled what documents were on the system and who had access to them.

Lobby group Digital Rights Watch has expressed concerns about the security of My Health Record, and is urging everyone to opt out.

"No guarantees have being given that individual citizen's personal information will be kept safe and secure," Digital Rights Watch chair Tim Singleton Norton said.

"Health information is incredibly attractive to scammers and criminal groups.

"There are also concerns of the current or future access being granted to private companies."

The Digital Health Agency said patients could switch off their entire record and make it only available using a pin code, or use that process with individual documents.

Opposition Leader Bill Shorten said the system was an important reform because it would lead to better health outcomes.

"But I don't blame people for being sceptical about this government in terms of the way it implements digital change programs," Mr Shorten told reporters in Tasmania.

The National Rural Health Alliance said it would save lives in regional Australia, and urged people not to opt out.

AMA President Dr Tony Bartone said privacy of medical records was "absolutely paramount" and the medical profession and federal government took it seriously.

"This is actually going to save lives - if someone was unconscious in an emergency department on the other side of the country, and you've got a My Health Record, it can be viewed in an emergency situation, give important clinical details about medications you're on or previous allergies or previous situations," he said.