More than 2.5 million Australians have opted out of the My Health Record system, new figures show.

The figures, revealed in Senate estimates on Wednesday, show almost one in 10 Australians eligible for Medicare have opted out of the controversial system.

The My Health Record’s opt-out period expired in late January, an extension of three months from the government’s previous planned date of 31 October. About 1.4 million people opted out in those three months.

Senate estimates also heard about 23.2 million Australians are now signed up to the system.

A further 300,000 people had cancelled their records, estimates heard. People can continue to cancel their My Health Record, despite the opt-out period finishing.

Health bureaucrats said the opt-out result was largely in line with expectations.

“That’s pretty much where we’ve landed: 90% of active Medicare users in Australia have not opted out,” the department’s deputy secretary, Caroline Edwards, said.

“So we’ll have My Health Records for 90% of Australians, for people with Medicare access.”

The My Health Record system is designed to allow information about patients to be shared between health providers, allowing continuity and better care. But the roll-out has attracted significant scrutiny.

Privacy and security fears were raised about the system, and glitches also prevented some healthcare providers uploading clinical documents to the system.

Labor’s shadow health minister, Catherine King, said the opt-out rate was a dramatic increase on the 1.15 million who had opted out of the system before the original planned end date.

“The government’s rushed implementation of an opt-out model created a range of problems and severely undermined public support for a system that could deliver enormous health benefits for all Australians,” she said.

Health bureaucrats also said a technical glitch affecting the system, which prevented clinical providers uploading information, had largely been resolved. The problem only “currently affects one-third of 1% of documents attempting to be uploaded”, estimates heard.

Guardian Australia revealed the existence of an internal briefing late last year that described the issue as “significant”, said it had been escalated to the minister, and was still not fully resolved. The problem, the briefing said, threatened to leave patients’ information incomplete or out-of-date.