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My Health Record changes pass upper house

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New penalties and stronger privacy measures for the federal government's My Health Record system have passed the Senate, after the government agreed to extend the opt-out deadline.

Health Minister Greg Hunt bowed to pressure on Wednesday, extending the last day people can opt out before their electronic health record is automatically created to January 31, 2019, from November 15.

Tighter privacy safeguards passing the upper house on Thursday.

The bill is now on course to be ticked off in the House of Representatives during the final parliamentary sitting fortnight of the year, which starts on November 26.

Under the changes, people found guilty of improper use of My Health Record would face up to five years in jail, instead of two, and the maximum fine would more than double to $315,000.

Victims of domestic violence would also be better protected, with abusive former partners banned from accessing their child's records.

Private health insurers would also be kept further from the system's data, being unable to access it even when it has been de-identified.

Mr Hunt said there was no deadline to leave the system, with people able to permanently delete their record at any point.

"At the end of the day, people can opt out at any time during their lives. That is one of the things which may not have been fully understood," Mr Hunt told the Nine Network on Thursday.

The opt-out period was meant to end on Thursday night, but Mr Hunt on Wednesday announced it would move to January 31.

If the date wasn't shifted, millions of Australians would have automatically joined the scheme.

© AAP 2018