The number of Australians who have opted out of My Health Record since July 16 has been revealed.

Australian Digital Health Agency (ADHA) head Tim Kelsey told a Senate inquiry into the medical database system on Monday evening that as of September 12, the opt-out rate was about 3 per cent — roughly 900,000 people.

He warned the estimate was not comprehensive and reflected only opt outs via the website or call centre, as paper forms had not yet been reconciled.

The opt-out period, which was extended after concerns from the medical community, ends on November 15.

Every Australian with a Medicare card will automatically be given a record unless they tell the agency they do not want one by the deadline.

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After the hearing, Labor health spokeswoman Catherine King said in a statement that the program's roll out so far was "botched", and called for it to be suspended.

My Health Record has been criticised by a variety of health and privacy advocacy groups during the opt-out period, prompting speculation about how many Australians would actively choose not to have one.

Mr Kelsey also said about 181,000 people had signed up since the beginning of the opt-out period.

Around 6.1 million Australians currently have a My Health Record, which existed as an opt-in system from 2012 until this year.

An ongoing privacy debate

Concerns about My Health Record raised before the Senate inquiry have focused on patient privacy, the system's security design, and access by third parties such as law enforcement.

My Health Record grants users a number of privacy controls over their medical records, but they are not in place by default.

In particular, users can set a code over the complete record or specific documents, limiting access to only those doctors with the pin code.

The agency told the committee that 16,848 record access codes and 4,109 limited document access codes had been set as of September 2.

It also said 136,644 people had turned on an email or SMS alert for when a new healthcare practitioner accesses their record.

In response to a question about whether these controls should be in place automatically, chief medical adviser for the ADHA, clinical professor Meredith Makeham, told the committee such a change could impact the system's effectiveness.

"The difficulty would be that with a record access control set as a default, the clinical benefit of the system relating to medications safety would be very much potentially closed down," she said.

"[Difficulty] would arise for a clinician who was trying to view the My Health Records of patients who were coming through, say, an emergency situation or through their rooms."

Access controls may be overridden in an emergency.

Leanne Wells, chief executive of the Consumers Health Forum of Australia (which has received funding from the ADHA), compared the project in scale to the introduction of Medicare.

"The community expects due diligence and vigilance … when it comes to safeguards," she said.

The committee also heard from the Australian Council of Trade Unions, which claimed legal loopholes could allow records to be accessed as part of pre-employment health checks by employer-nominated doctors — and by extension employers — among other scenarios.

"Additional amendments are required that make it clear that records cannot be accessed for employment purposes, to protect MHR [My Health Record] data being used for commercial purposes and to place obligations on the database operator as well as those who access it," an ACTU spokesperson said.

Mr Kelsey said no My Health Record data has been disclosed for employment purposes.

Former Digital Transformation Office boss Paul Shetler told senators that time should be taken to "reset" the system.

"In its current form, I believe the program will fail," he said.

Following concerns from health and privacy groups, Health Minister Greg Hunt proposed a legislative amendment in late July to clarify that no health information in a My Health Record could be disclosed to law enforcement agencies and government agencies without an order by a judicial officer or the user's consent.