The admission comes as Canberra emergency departments recorded their busiest year on record, with staff treating nearly 130,000 patients during 2014-15, or an average of 357 presentations a day.

The number of people visiting the departments has increased by 22 per cent since 2009-10, despite the territory's population growing by 9 per cent.

The Auditor-General's report, published in July, warned of insufficient controls to detect missing data, duplicated data, and data entered in the incorrect period.

In 2012, the government faced allegations of "data doctoring" in territory health services after it was revealed patient records had been manipulated to improve reporting outcomes.

ACT Auditor-General Maxine Cooper acknowledged ACT Health had made "considerable efforts" to improve processes in recent years but made 18 recommendations, with nine classed as a high priority.

Health Minister Simon Corbell welcomed the report, agreed with all recommendations, and insisted many were already implemented with work under way for others.

"The report did note that additional work is required in relation to non-admitted data quality processes as well as general data quality assurance activities," he said.

"ACT Health will implement improved data standards and better data quality assurance processes that increase the confidence in the information within ACT Health."

Mr Corbell said the department would not miss out on any Commonwealth funds as a result of the data errors, as they would be rectified in a final submission to the federal government in September.

The Auditor-General recommended names and explanations be attached to any changes to emergency department records, automated checks for inappropriate patterns, and a single dictionary for data entry at both hospitals.

"The government is serious about emergency department data integrity," Mr Corbell said.

"Initial work has been completed to provide additional audits of activity within the emergency department as well as the initiatives already in place that minimise access to the system and minimise the possibility of inappropriate changes being made without a clear audit path."

Mr Corbell said changes to data logging procedures were desirable but needed to be balanced with the challenges of treating a growing number of emergency department patients.

According to figures detailed in the ACT Legislative Assembly by Labor's Megan Fitzharris, 129,963 patients were treated by the two departments in 2014-15: a three per cent increase on the previous year.

"This was the highest number of presentations recorded in a single year," she said. "There are a range of reasons for the increasing demand on services and they require a range of solutions.

"It is essential that we have an understanding of what we are dealing with in terms of the reason for the growing demand on all of our services so that we can plan for the future."

Ms Fitzharris said it was unfortunate many Canberrans still had to consider the costs of visiting a doctor and these hesitations may have prompted many to visit the emergency department.

In February, a Productivity Commission report on government services found the availability of GPs per 100,000 people in Canberra had increased from 65.5 in 2010-11, to 72 in 2013-13.

"That same report found proportion of Canberrans who report they deferred visits to a GP due to cost is the joint highest in the nation at 6.9 per cent," Ms Fitzharris said.

"We know these people come to emergency departments when they could be getting care elsewhere."

The ACT government has committed $23 million to an extension of the Canberra Hospital emergency department, which would increase the number of beds by more than a third.

Mr Corbell has described the extension, which was already begun, as a "short- to medium-term response" as the government considers redeveloping other buildings at the hospital.