Health minister Greg Hunt last week unveiled changes to the scheme to address a range of concerns about privacy, such as whether violent exes would be able to access the records of their former partners.
A Senate Committee called for changes to the legislation underpinning the record after hearing concerns that employers may try to get access to employees' My Health Record.
The amendment wouldn't have become law before Thursday night's deadline, prompting the minister to step in and extend the date.
Labor's push to have the deadline extended by 12 months was denied before One Nation's amendment for a January 31 deadline was approved.
"Labor's plan to delay and derail the roll out of the My Health Record was blocked today", Mr Hunt said in a statement.
The scheme was launched under the Labor government in 2012 as the Personally Controlled Electronic Health Record.
The deadline to opt out of the My Health Record system has been extended by two-and-a-half months, meaning millions of Australians will no longer automatically join the scheme by the end of the year.
"For example, you could have a podiatrist or a physiotherapist viewing sensitive information about your mental or sexual health".
Ms King said she hoped the extra time would allow federal parliament to refine the system to address privacy issues.
"To my knowledge, there is now no public disclosure of the precise security controls and technologies deployed for My Health Record, nor have audits been published or even their summaries", Ralph Holz, an expert in cybersecurity from the University of Sydney, tells The Daily Swig.
Ben said he just wanted to wait until after legislation passed that would improve privacy and security for patients before opting in.More news: Warriors' Green not apologizing, he and Durant moving on
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"My Health Record was created to save lives".
Legislation that would ensure a patient's right to permanently delete their record and that police can only access someone's medical history with a court order, have not yet been passed.
People can access their data online at anytime and can adjust how it may be viewed by health professionals and people they trust.
It came after a number of Labor and crossbench members voiced concerns about both the unresolved privacy and security issues around the system, and the difficulties faced by users from early in the week in opting out.
Proposed legislation will also stop private health insurers or other insurers from seeing the system's data for research or public health purposes, even when it has been de-identified.
Health Minister Greg Hunt announced the extension on Twitter this afternoon, saying the government had "worked with the senate crossbench to extend the opt-out period for My Health Record".
After the opt out period, parents or guardians of newborns will be able to opt out of having a My Health Record created for their child as part of their child's Medicare registration.
The motion by Senator Hanson to extend the opt-out period was unopposed, but is not binding on the government as the House of Representatives - which is not sitting this week - would first have to approve it.
New penalties for those who misuse the system and better privacy protections are set to be debated in the Senate this week. Tech experts from Melbourne University showed in 2016 how easy it was to re-identify Medicare data and they say it is nearly impossible to fully de-identify health data.