The change of deadline coincided with an extended period of degradation on the My Health Record opt-out site on the eve of the close of the opt-out period. It won't be done before the November 15 deadline for opting out. However minutes later, an amendment moved by One Nation leader senator Pauline Hanson for the January 31 extension was passed on the voices.
"Labor's plan to delay and derail the roll out of the My Health Record was blocked today", Mr Hunt said in a statement.
Labor's health spokesperson, Catherine King, said it would be "scandalous" if Hunt did not accept the Senate's bill, especially after the system crashed from today's demand.
About four per cent of Australians (1.147 million) have so far opted out of the electronic health record system, while more than 300,000 have opted in during the opt-out period which ends on Thursday.
These data breaches included unauthorised access, fraud and the wrong health information being added to My Health Records.
The extent of the breaches to hit the My Health Record has been revealed by the Office of the Australian Information Commissioner.
Ms King said she hoped the extra time would allow federal parliament to refine the system to address privacy issues.
Ben said he had tried opting out on the website first and was successful completing the process for his own record and one of his sons.
The Australian Digital Health Agency, which is responsible for the My Health Record, also explained that Australians have greater ability to personally control their digital health information than other countries around the world. "It can help prevent medication misadventures that see more than 230,000 people end up in hospital each year", he said.
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The system - which is an online summary of an individual's health information, including allergies, medical conditions, treatments, medicines and test reports - raised concerns about the level of security and privacy surrounding the data.
People can access their data online at anytime and can adjust how it may be viewed by health professionals and people they trust.
Cyber security expert Nigel Phair, from the University of New South Wales, said the overall My Health Record database was unlikely to be hacked but he predicted data breaches would occur around compliance and governance of the system, including doctors potentially viewing records they shouldn't out of personal interest.
They include strengthening the safeguards in cases of domestic violence; banning employers from requesting and using private health information; and banning health information being released to insurers, even if de-identified.
While the legislation now has to pass the lower house, where the government has lots its majority, which doesn't sit again until November 26 - 11 days after the current opt out deadline - Health Minister Greg Hunt announced within hours of the vote that he would agree to the January 31 extension.
The ADHA said people experiencing long wait times on the hotline could opt to be called back, and no record would be created in the meantime.
"The Guardian reported that the motion calls for the opt-out period to be extended 'until the legislation and any amendments are passed, outstanding privacy and security issues are addressed and public confidence in this important reform is restored".
It includes harsher penalties for people found guilty of improperly using the system, and better protections for victims of domestic violence. There are fines of $126,000 and up to two years' jail time for people who breach the record, and these will soon be increased.