"I have a condition called hydrocephalus, which basically means that I have too much fluid in my brain," Mr Toohey said.

"It can cause severe headaches and other symptoms as well. I had four days in Canberra Hospital because I had a migraine that was so bad [doctors] thought I had a stroke."

Despite the complexities of his medical condition, the Narrabundah resident said he does not want to have a personal health record detailing his medical history stored online.

Mr Toohey is one of thousands of Australians who have already opted out of the federal government's My Health Record scheme.

An online medical record will be created for all Australians, unless they opt-out before October 15.

The opt-out period began on Monday, with an estimated 20,000 people electing to not store their records online on the first day alone.

The system will allow for records to be accessed by almost 13,000 health organisations and up to 900,000 health professionals.

While Mr Toohey said such a scheme could be helpful to those with complex medical conditions or for those who change GPs or addresses, he said he's worried about a potential data breach.

"I don't think there are enough protections there and I'm also concerned about the privacy," he said.

"Not enough has been done to assure us that the data will be secure and won't be used for purposes other than that of health professionals.

"The concept is good, but the execution of it is poor."

It's estimated almost 6 million Australians already have a My Health Record created.

A spokesman for the Australian Digital Health Agency said de-identified data will only be used for population health research and health services planning, and no information will travel between the parties until at least 2020.

"My Health Record is built with strong privacy and security features including strong encryption, authentication, firewall protection and is protected by law," the spokesman said.

"We actively monitor and respond to threats and risks within the cyber security environment. To date there has never been a security breach of the My Health Record system."

Those with a record can receive information on healthcare providers who view their information, with penalties of $126,000 and up to two years in jail if a person accesses a record without authorisation.

The spokesman for the agency said many authentication steps are in place in order for a doctor to view a My Health Record.

The privacy concerns surrounding My Health Record comes as a new consumer survey of more than 2000 people from comparison website finder.com.au revealed 68 per cent of people with health insurance had no problems in handing over medical history to providers for cheaper insurance.

Insights manager Graham Cooke said 70 per cent of women and 65 per cent of men would be willing to divulge their medical records, according to the survey.

"The new system of giving the government access to personal data does raise the question about privacy," Mr Cooke said.

"However, it shows that a monetary incentive goes a long way, given the majority of ACT residents are willing to give up their health information in exchange for lower insurance premiums."

Mr Toohey said while he will still have many checkups and medical tests in coming months, he's not prepared to have his medical history online.

"It would be very useful to have that sort of information to different people treating me, but I'm still not prepared to run the risk of a breach of privacy."