Federal Health Minister Greg Hunt has extended the deadline for opting out of the Government's contentious My Health Record system.

Key points: Government is giving Australians 10 weeks more to opt out

Government is giving Australians 10 weeks more to opt out Decision follows reports of difficulties in opting out due to website and telephone issues

Decision follows reports of difficulties in opting out due to website and telephone issues Parliament will continue to debate the legislation

He confirmed the delay on Twitter within hours of the opt-out website suffering issues and the Senate agreeing to an extension.

"The opt-out period will be extended until January 31, 2019, however, it's important to note that people can opt-out at any time," he said.

The opt-out website suffered issues on Wednesday morning as Australians tried to remove themselves from the scheme ahead of the previous deadline, which was set to expire at 3:00am (AEDT) on Friday.

The Senate is currently debating the legislation, but already agreed to extend the opt-out deadline to the end of January.

The amendment needed to return to the House of Representatives to be formally adopted into law, but Mr Hunt intervened to extend the cut-off.

Greg Hunt previously dismissed calls for an extension to the deadline. ( ABC Mildura Swan Hill: Jennifer Douglas )

Every Australian with a Medicare card will automatically be given a digital record to store medical information uploaded by their health providers unless they opt out before the deadline.

The site appeared to be unavailable to some users on Wednesday morning. It became available again at approximately 12.30pm, but throughout the afternoon people continued to report technical issues.

There have also been complaints about difficulties opting out via telephone.

But the agency responsible for My Health insisted the website and telephone helpline were both "operational".

"We are experiencing high demand, which has slowed the system down, and some people have experienced difficulties opting out this morning," an Australian Digital Health Agency spokesperson said in a statement.

"These issues have now been resolved.

"The agency anticipated higher call volumes and has increased the number of helpline operators available to support callers."

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'Let's get this right'

The Government had repeatedly refused to extend the opt-out period, until Mr Hunt took to Twitter on Wednesday afternoon.

"The Government's focus is on strengthening the safety and privacy of health information in the My Health Record system," he said.

"The Parliament is now considering further amendments to Labor's original My Health Record legislation."

Labor's health spokeswoman Catherine King still has concerns about data security and privacy and wants the Government to extend the opt-out deadline for 12 months.

"Let's get this right, we think this is an important reform, it was a reform started by Labor but we think you need to take the time to get this right," she said.

"We have been forced into the position today in the Senate of trying to extend the opt-out period again because the Government is just not listening."

More than 1.1 million Australians had elected to opt out as at the end of last month.