Australia's Human Rights Commissioner has urged the Federal Government to make changes to the My Health Record to restore confidence in the privacy and security of the system.

My Health Record is a digital database containing the medical records of every Australian who does not opt out by mid-October.

Human Rights Commissioner Edward Santow has concerns about the system and wants the Government to improve privacy protections.

"I think we can do better," he told AM.

"We definitely are saying that there are problems with My Health Record."

Mr Santow urged the Government to boost the system's security to make sure it was not vulnerable to being hacked or misused.

He also called for more work to be done to ensure people understood how their personal information would be used.

The Commissioner said if those goals were achieved, people would be more likely to accept the idea of sharing data on the My Health Record system.

Mr Santow said people's concerns included that someone who was slow to pay a healthcare bill could have data from their My Health Record used to chase the debt.

"That is not necessarily something that people would willingly sign up to," he said.

Human Rights Commissioner Edward Santow said the key to people accepting the new system was to give them confidence in it. ( Supplied: Australian Human Rights Commission )

A range of people have spoken out against the new system, including Liberal backbencher Tim Wilson and former Queensland LNP premier Campbell Newman.

Mr Newman urged people to opt out of the system which he labelled "unAustralian".

"The idea that public servants and other departments and statutory bodies should be able to get into your information is completely unacceptable, it is just not on," Mr Newman said.

Mr Santow said people wanted control over the way their personal information was used, and said the problem with My Health was that it reduced autonomy.

In defending the program, Health Minister Greg Hunt said it had been operating in an earlier form for six years and added that 6 million patients were already online.

"It's operated without issue and that continues to be the case," the Minister said.

The ABC has revealed the Government is scrambling to put new restrictions on mobile phone apps that offer access to the My Health Record system.

The Digital Health Agency wants the power to cancel those companies' contracts more easily if their actions damage confidence in the My Health system.

Hunt dismisses complaints about not being able to opt out

Mr Hunt stressed it was up to consumers to decide whether they used those apps and said people's health data would not be given to companies without their consent.

Mr Santow said the key to people accepting the new system was to give them confidence in it.

He said if they feared the information might be used, "for some secondary purpose against them — that is where we have a problem".

"That is where we need to be better protecting people's basic rights," Mr Santow said.

Mr Hunt also dismissed complaints about people not being able to opt out on the My Health Record website.

One person told the ABC they had tried to opt-out, "once last week and twice on the weekend and all three attempts failed".

But Mr Hunt said: "The system has been working continuously.

"What might happen is that people could have a session timeout or an internet dropout or open more than one internet browser window," he told Sydney radio station 2GB.

Based on current projections, the Health Minister said no more than 10 per cent of people would opt out.