The multi-million dollar system-wide data review was supposed to inspire greater confidence in the reliability and accuracy of the health directorate's data, after years of problems culminated in the territory being unable to submit key metrics to the Productivity Commission.

But ACT Auditor-General Michael Harris has criticised the project implementation team for poor planning and documentation.

"Planning for the implementation of the System-Wide Data Review program is not effective," he said.

"There is neither transparency nor clarity about how and when the three-year program will be delivered and if the program will be completed as envisaged."

The audit found the project was being planned in six-month blocks, with no timeline set out beyond June 2019.

This failure to plan for the long term "increases the risks of a poorly executed ... implementation program and not realising the benefits anticipated from the three-year program of work", Mr Harris said.

ACT Health told the audit office its programs were "living documents" and as stage two was only commencing "activity reprioritisation has not occurred to date".

But Mr Harris said there were no specific deadlines for tasks to be completed, and no way of tracking tasks from the first stage that may bleed into the second.

Mr Harris also said it was unclear what sort of money and people were being put towards the project, as it was being carried out within the existing resources and did not have a separate, identifiable funding allocation and associated budget.

This meant ACT Health was not planning for or tracking the costs of the project against a set budget.

Failure to do this meant "the ACT Health Directorate cannot effectively manage future costs", Mr Harris said.

The roles and responsibilities of the program manager responsible for the rollout were not documented, although could be "surmised from a range of other documents" which could lead to "misunderstandings about responsibilities and inconsistencies in the way in which the roles are carried out".

Furthermore, one of the two working groups set up to oversee the project's rollout is yet to met, despite being convened in October.

The working group that has met took three months to finalise the terms of reference of their group, which Mr Harris said "represents a missed opportunity to have robust and formalised governance arrangements from the outset of the implementation program".

ACT Health chief information officer Peter O'Halloran, acknowledged there were areas that needed improvement.

However he said the audit was done early on in the project and "critically important components" like the data repository were on track.

"Since the audit was carried, further improvements have been made and we have released our Phase Two Review Implementation Plan," he said.

"We have also reached a key milestone with the launch of the ACT Health mobile phone app, which has been downloaded by over 4000 people and is growing every day."

But Canberra Liberals' health spokeswoman Vicki Dunne said the audit highlighted "another leadership failure from this minister".

"The whole reason modern health systems collate health data is to ensure the delivery of safe and efficient health care," she said.

The audit caps off years of data troubles within the health directorate.

In 2012, a hospital executive was exposed as doctoring thousands of emergency room figures to make them more favourable.

In 2016, 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 had been repeatedly changed.

Then in 2017 Health Minister Meegan Fitzharris admitted the government had been unable to meet deadlines for several key reports because of concerns around the accuracy of some of its data.