ACT health minister Meegan Fitzharris has ordered an urgent review into ACT Health's data collection after the department failed to provide figures on its emergency department to the Productivity Commission for its annual comparison of the performance of states and territories.

Ms Fitzharris said ACT Health was unable to meet reporting deadlines because of concerns around the accuracy of the data. A spokeswoman for the minister said these inaccuracies were not deliberate.

But the minister maintained the issues were "administrative in nature" and would not affect frontline health services.

She said the ACT would not lose Commonwealth funding for its hospitals despite missing the deadline.

However the concerns around data accuracy recalled the data tampering scandal of the Gallagher government, when an ACT Health employee was stood down after allegedly manipulating Canberra Hospital emergency department waiting time data.

More than 11,700 patient records were doctored between 2009 and 2012 to make the performance of the emergency department look better.

Last year, the government was forced to correct misleading data on the performance of Canberra's public hospitals, after it was revealed median wait times at emergency departments during July-December 2013 have been repeatedly changed by ACT Health in recent years.

Ms Fitzharris said while ACT Health had been "proactive" in recognising the problem this time around, the department needed time to ensure its data management and quality assurance processes were "robust and accurate".

She said ACT Health's director-general ordered an internal review into the accuracy of the department's data after last year's budget estimates.

PricewaterhouseCoopers (PwC) was called in to review the accuracy of the data. The minister did not detail its findings.

However, she said the review meant ACT Health was unable to meet reporting deadlines from the Productivity Commission and the Australian Institute of Health and Welfare.

As such there were gaps in the data on public hospitals and mental health services, Ms Fitzharris said.

"That's I why I have asked for a comprehensive, system-wide review that takes us back to the basics of the collection, analysis and reporting of our health data," Ms Fitzharris said.

"I want to be very clear that although data reporting issues are administrative in nature and do not affect the quality of health services we deliver.

"As minister for health I know how important it is that the community, our patients and our health sector stakeholders have confidence in health reporting.

"I remain committed to providing data that accurately reflects the demand for, and performance of, the services that are provided in our hospitals, health care facilities and throughout our program."

The review will examine the structure of the department responsible for data governance, undertake "integrity validation checks" and develop a formal process for amendments to reporting.

The ACT Auditor-General will be involved in the review.

A spokesman from the audit office said audits on health directorate data had been undertaken in 2012 and 2015 and the auditor-general was "currently considering a range of information to determine if a performance audit should be undertaken".

Earlier this month the Canberra Liberals raised questions about why the ACT government was the only government in Australia that failed to supply data to the Productivity Commission on the proportion of emergency department patients seen within triage category timeframes.

Liberals' health spokeswoman Vicki Dunne had called on Ms Fitzharris to make the figures public.

In the assembly on Tuesday, Ms Dunne said the minister's statement "raised more questions than it answered".

"We need to know exactly what the problems in the data are," Ms Dunne said.

"The minister should not have waited until the public was alerted through the absence of data in the [Productivity Commission] report, the minister needs to come clean with the assembly and say when she knew there was a problem with the data."

Australian Medical Association ACT president Dr Steve Robson said he had written to ACT Health's director-general about the missing data weeks ago but failed to receive a response.

He said it "wasn't quite right" to say the inaccurate data would not affect frontline services.

"I think it's critical to know the care that's being provided is measurably appropriate and the only way you can do that is the careful analysis of data," Dr Robson said.

"Will it stop you getting a clinic appointment? It probably won't but the question is are the clinical services providing care that is the best possible standard? The only way we know that is by the accurate collection, analysis and comparison of data."

Dr Robson said problems with data accuracy "goes to the heart of the delivery of care and the confidence the community has in its health services".

"The public have a right to reassurance that their healthcare systems, particularly in this case public hospitals, are appropriately benchmarked, that they're appropriately compared to services elsewhere in the country," Dr Robson said.