The federal government appears unlikely to extend the My Health Record opt-out period, despite Labor calls for a longer period to allow new protections to be made law.

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.

However, the final opt-out figure is expected to hit 10 per cent.

New penalties for those who misuse the system and better privacy protections are set to be debated in the Senate this week.

But the House of Representatives won't sit again until November 26 to consider any Senate amendments.

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Health Minister Greg Hunt argues there have been no cases of misuse of information in the six years the system has operated, but the government was still willing to provide further protections.

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.

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The Senate on Monday passed a Greens and Labor motion seeking an extension of the opt-out period.

The motion called on the government to "extend or suspend the opt-out period until the legislation and any amendments are passed, outstanding privacy and security issues are addressed and public confidence in this important reform is restored".

Labor's health spokeswoman Catherine King says the system promises huge benefits to Australians who choose to participate, but the government had botched the rollout and undermined trust in it.

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Once the opt-out period ends the government will begin creating records for 17 million Australians, whether they want one or not.

However, Australians will be able to have their record deleted after November 15.