Another 1.4 million people decided against having a digital health record during the three-month extension to the My Health opt-out period.
New figures show more than 2.5 million people have opted out of My Health, with the majority making the decision during the three month extension to the deadline.
Senate estimates heard on Wednesday that about 1.4 million chose to opt-out between the original deadline of October 31 and the extended date of late January - bringing the total number of Australians who won't have a digital health record to 2,517,921.
Health department officials told the hearing the vast majority of Australians would be included in the new system.
"That's pretty much where we've landed, 90 per cent of active Medicare users in Australia have not opted out," the department's deputy secretary Caroline Edwards said.
The digital system is designed to allow patient's medical information to be shared between hospitals and other health providers, but the roll-out has been hampered by concerns about privacy and security.
Another estimated 300,000 are believed to have had records and cancelled them.
Labor's health spokesperson Catherine King blamed the number of opt-outs on the government's "rushed implementation".
"The government’s implementation of the My Health Record has been a complete debacle from day one," Ms King said.
Ms King is calling for an independent Privacy Commissioner to conduct a review examining issues including protections for vulnerable people and measures to encourage consumer engagement.