A report published on Thursday found the average cost of care for an acute patient at the Canberra Hospital was $6500, which was 76 per cent higher than the best performing metropolitan hospital in Australia.

Calvary Hospital ranked second in comparable costs at $6300, which was well above the national average cost of $4900 per patient in metropolitan hospitals.

The report comes after The Canberra Times revealed emergency patients admitted to ACT wards cost twice as much to treat than similar patients in South Australia, Victoria and Tasmania.

According the report, the Canberra Hospital also has the highest cost per national weighted activity unit at $5800, which was 87 per cent higher than the best performing hospital.

The report, which was prepared by the National Health Performance Authority, called upon 2011-12 data and did not access the quality of care provided.

"As a result, it is not possible to conclude whether a hospital with lower or higher cost per unit of activity provides better or worse health outcomes than other hospitals," the report said.

ACT Opposition Leader Jeremy Hanson said the data revealed the territory's health system was lagging behind the rest of the country.

"Inefficient costs mean funding is directed away from other areas of the health system which need addressing," he said.

"In only the last few weeks, concerns have been raised about the ad hoc approach to fixing the emergency department at the Canberra Hospital while there are questions about the government cutting bed numbers at the proposed University of Canberra hospital."

But Australian Healthcare and Hospitals Association chief executive Alison Verhoeven said costs were only one measure of hospital performance and should not be confused with quality.

"While information on hospital cost variations is useful, particularly to identify opportunities for greater efficiency, we cannot make judgments about hospital performance without also considering data on the quality of care and patient outcomes," she said.

ACT Health Minister Simon Corbell said the comparison between Canberra's hospitals and those in other cities was not an even comparison.

"ACT public hospitals provide a wide range of healthcare services to the community, due to the ACT accepting many of the more serious patients from our surrounding NSW region," he said.

"This includes high-cost services such as open heart operations, bone marrow treatment and intensive care services for babies."

An Independent Hospital Pricing Authority spokeswoman said the report demonstrated an "extensive variation in public hospitals across Australia, although the situation may have improved since 2011-12''.

"The growth in costs in public hospitals across Australia has slowed considerably such that there is very little growth in the national average costs of public hospitals from 2011-12," she said.

AMA president and associate professor Brian Owler said the report would allow hospitals to assess their performance on a costs basis and identify variations.

"These could range across all cost elements and cost drivers that contribute to the cost of patient care, including administration, staff and clinical costs, average length of stay, [and] other variations in local procedures and practices," he said.

"The report does not examine the quality of care provided and the health outcomes experienced by patients. These could be both a contributing factor and a consequence of different costs of care."

Mr Corbell said labour costs and reporting standards could also give rise to differences in patient costs across the country.

"This is particularly the case in the ACT with higher wage costs reflecting higher prices in general in the territory compared with elsewhere," he said.

"A significant difference between the cost figures for ACT hospitals and those in other states is that those in the larger states share their corporate overhead costs across numerous hospitals, while in the ACT these costs are spread across only two large public hospitals."