Rachel Stephen-Smith says workers had warned about data reporting risks of digital health record

Rachel Stephen-Smith told budget estimates there were workers who had expressed concern at the time it would take for health officials to be able to properly report on performance data.

Data including average emergency department wait times and elective surgery waiting lists have been unable to be reported on since the digital health record was implemented last November.

The digital health record collated all paper and digital records in the territory's public health system under the one electronic system.

The government has said processes for the collection and collation of service data are still under development.

Ms Stephen-Smith said these concerns at the length of time had not been properly escalated through the project team.

"I'm not sure that the level of just how long it was going to take to resolve this issue had flowed through to me," Ms Stephen-Smith said.

"I think the extent of the challenge was probably something that was better understood on the frontline than it was by me at the time of go live."

However, Ms Stephen-Smith said she was aware there would be issues and she said the system had to go live in order to identify what these would be.

"I definitely know that there were going to be issues with the data, that was absolutely clear in the briefings," she said.

"We also knew that many of those challenges could not be resolved and we actually had to go live in order to address those challenges."

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Canberra Health Services chief executive Dave Peffer said it was "enormously complex" as the system was used differently by individuals and the data had to be cross checked to ensure it was correct.

He said the same issues would have existed no matter when the system was implemented.

"If we worked on this for another 12 months and then went live it would be the same issue," Mr Peffer said.

Freedom of information documents showed Ms Stephen-Smith was told in a briefing there was a risk the ACT would not be able to meet national reporting deadlines for agencies such as the Australian Institute of Health and Welfare and this could pose a risk for reputation and funding.

Ms Stephen-Smith said she was hopeful this data could be reported by September when it was required.

The ACT was the first place in Australia to roll out such a system all at once and other jurisdictions had rolled out systems either in one hospital or in one health district at a home.

Opposition health spokeswoman Leanne Castley questioned why the territory had to do it all at once. She has asked the Auditor-General to examine the implementation of the digital health record.

"I thought it was really disappointing to hear that they were warned and didn't understand [and] there was a little bit of confusion," she said.

"It is disappointing for Canberrans because this is important data that informs federal funding and it helps us understand how we're tracking within the hospital system.

"We know things have been problematic and we really need this data."

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