But Health Minister Greg Hunt has stressed there really is there no single deadline to leave the system, with Australians 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.

"There is no single deadline."

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

The decision came after legislation strengthening privacy protections for the electronic health record system was amended in the Senate to include the extension.

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

The extension also gives the government time to pass legislation before the Senate which toughens safeguards around people's health data.

Changes to the scheme include tougher penalties for people who misuse the system and stronger protections against people's health records falling into the wrong hands.

One Nation leader Pauline Hanson, who moved the Senate amendment to extend the date, said website crashes had made it difficult for some people to opt out.

"I believed it was only fair and reasonable to extend the initial opt-out period," Senator Hanson said.

Incoming independent MP and former Australian Medical Association Kerryn Phelps backed the extension, saying there are critical privacy and security safeguards still to be legislated.

"The government must now use the final two sitting weeks of 2018 wisely because that is the only opportunity before the new deadline to get the settings of My Health Record right," Dr Phelps said.

Australian Associated Press