It is further understood that from December only one existing, dedicated privacy staff member will remain at the organisation, with one leaving the business to move overseas and another going on 12 months leave. At its peak, the privacy team consisted of four people.

“The agency as a practice does not comment publicly on staffing matters,” an ADHA spokesperson said. “The agency has an experienced and well-resourced privacy team."

Asked if ADHA would replace Ms Hunt, the spokesperson said it had restructured its privacy team to report to another director.

“The agency … has recently announced an internal restructure ... to ensure the agency is the right size and shape beyond the opt-out program," they said.

"These changes have not significantly changed the staffing profile or resourcing of our privacy team, but has brought the policy and privacy functions under one director position."

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ADHA declined to state which director the privacy team would now report to, saying: "The agency has nothing further to add."

Two sources close to Ms Hunt confirmed that she had left the business out of frustration that privacy and security concerns her team had raised with senior management were often ignored.

“ADHA's privacy staff are very disillusioned that their advice and that of external privacy experts has not been listened to,” one source said, adding that there was a pattern of “not listening” at senior levels at ADHA and within Health Minister Greg Hunt's office, and that concerns were treated simply as management or public relations issues.

Said a second source: “I don’t think you are on the wrong track with the 'not listening'. They are hearing, they are listening to something, but they are reconfiguring it into another conversation; and it is not the conversation the Australian public want to have."

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Anna Johnston, director of privacy consultancy Salinger Privacy and a former NSW deputy privacy commissioner, said the resignation and claims of not listening were not a good look, nor was consolidating the role of privacy director with another director with other responsibilities.

“No longer having a director leading a separate privacy team outside of the broader policy area suggests to me that ADHA does not properly value the critical judgment and expertise that an independent chief privacy officer can bring to an organisation,” Ms Johnston said.

Following publication of the news of Ms Hunt's resignation on Friday, Labor's shadow health spokeswoman Catherine King said it was "extremely concerning" and showed "why we need a Privacy Commissioner review of the My Health Record".

About 17 million Australians will be automatically enrolled in the My Health record if they do not opt-out by next Thursday, despite lingering significant privacy concerns.

On Tuesday, Health Minister Hunt unveiled long-awaited changes to the government's My Health Record legislation to address privacy concerns, protect young people and domestic violence victims.

Separate legislation that would enshrine a patient's right to permanently delete their record, and ensure that police may only access a person's medical history with a court order, is yet to pass Parliament but politicians will not get a chance to debate the bill before the opt-out deadline.

A Senate inquiry into the rollout of the e-health system last month recommended that the opt-out period be extended by 12 months, but the extension was refused.

with Dana McCauley

Australians who want to opt-out can do so using their Medicare details and personal identification through the My Health Record website, help line 1800 723 471 or print forms at post offices.