ACT's health system has faced significant problems with data since it was revealed in 2012 emergency department data had been manipulated.

Then, in February 2017, an urgent review of ACT Health's data was ordered when the department failed to submit data to the federal government due to "accuracy concerns".

It meant its performance could not be compared to its peers across the country.

A number of reviews and audits have followed and the government was unable to produce quarterly reports for two years.

The ACT Auditor-General recently found problems with ACT Health's system wide data review, saying it lacked transparency and clarity about how data upgrades were being delivered.

Answers to questions taken on notice at estimates hearings last month have revealed the government plans to spend $12.6 million by 2020 on fixing the data problems, with spending beginning in 2016.

The cost to fix data problems was highest in 2017-18, when the government spent almost $4 million.

Before the 2016-17 financial year, the government did not spend any money on improving health's data.

"The government's lack of integrity in the management of health data has been diabolical," opposition health spokeswoman Vicki Dunne said.

"It is costing both health consumers and taxpayers dearly.

"Canberrans are now paying a very high price to clean up this mess, without any guarantee that the problems will ultimately be resolved.

"Of course, the real victims of the ongoing data scandal are patients. Health data is critical to the delivery of safe and efficient health care. Inaccurate or missing health data undeniably compromises patient safety.

"I have no doubt that many patients have actually endured prolonged suffering because inaccurate, manipulated or missing health data has compromised the delivery health care."

An ACT Health spokeswoman said data issues had never affected patient safety.

"It was about the processes for quality assuring and reporting the data externally. Health staff have always had access to the data they need to deliver their services," she said.

She said since 2017 there had been significant work to improve health data.

"Reporting good quality data about our health services and doing this in a timely way, is something we want to get right," the spokeswoman said.

"Since 2017 there has been significant work to improve our processes and we are on track in terms of the rigour of our governance for our data repository - a critically important component of our data collection and analysis.

"In saying this, we know there remains areas for improvement, and we will continue to focus on this as we implement recommendations of the System-Wide Data Review.

"Earlier this year, we reached a key milestone in regards to providing the community with better access to information on our services, with the launch of the ACT Health mobile app."