According to a National Health Performance Authority report, Canberra Hospital almost twice as much on acute care per patient ($6100) than similar hospitals in Melbourne.

Calvary Hospital ranked second at $5800 per patient, which was well above the national average of $4420 in peer hospitals.

The 2013-14 figures were calculated by comparing running costs with hospital output, but they did not assess the quality of care provided by medical staff. Equipment and building costs were excluded to ensure comparability.

The report reveals the cost of care at Canberra Hospital has increased by 7 per cent since 2011-12. It also shows Calvary Hospital is one of only six major metropolitan hospitals to have recorded a cost increase of 10 per cent or more.

A separate report released by the NHPA on Thursday found those who delayed visiting a GP due to cost were more likely to visit an emergency department.

Patients with three or more long-term health conditions were almost three times more likely to visit an emergency department than those with none.

Health Minister Simon Corbell said the cost difference could be explained by a range of factors, including higher average salaries for clinical staff, and one-third of staff remaining on generous legacy Commonwealth superannuation schemes.

"Specialist services, such as open-heart surgery, some complex brain surgery, bone marrow transplantation and some high-level care for babies offered in the ACT do not have the same economies of scale possible in larger jurisdictions," he said.

ACT Australian Medical Association president Dr Liz Gallagher said the report should be treated as a discussion starter rather than a report card.

"This is purely a descriptor, and there are a lot of aspects that are not explored by the report, but it should be used as a basis for continuing discussions," she said.

"We know hospitals in the ACT have been among the most expensive for some time, and ACT Health is looking to improve efficiency, but this report is limited in scope and does not cover clinical outcomes."

ACT opposition leader Jeremy Hanson said the report showed disgraceful management of the health system.

"Tens of millions of dollars that could otherwise be reinvested in hospitals are instead being wasted because our hospitals are not being run as efficiently as like hospitals interstate," he said.

"The health system needs to be bigger, with more beds in more locations, it needs to be smarter, with a greater emphasis on early intervention and preventative health, and it needs to be better, providing an improved culture for staff and better patient care."

Mr Corbell said the government was conducting an innovation review to strengthen the delivery of health care, including changes to how patients access care, and delivery solutions.

"ACT Health, like all areas of the ACT government, is expected to manage the provision of services within its budget and to increase efficiency in its operations where possible," he said.

This month, ACT Health director-general Nicole Feely wrote to senior health executives urging them to make "judicious workforce management" their number one priority.

Australian Healthcare and Hospitals Association chief executive Alison Verhoeven said more work was needed to improve efficiency.

"Variations in costs of care across hospitals and jurisdictions should continue to be the focus of efficiency programs, although consideration must be given to factors such as service volume and workforce costs, which vary across hospitals and are not taken into account in this report."