A National Health Performance Authority report to be released on Thursday reveals 54 per cent of Canberra Hospital patients last year completed their emergency department visit within four hours, compared with 66 per cent at Calvary Hospital.

The data indicates there was a slight improvement on 2012 figures, when 52 per cent of Canberra Hospital patients left the ED within four hours, compared with 63 per cent at Calvary public.

The report reveals that patient numbers were also up from 53,592 at Calvary public in 2012 to 53,847 last year, compared with an increase from 66,069 in 2012 to 68,033 last year at Canberra.

The annual target for the ACT was 64 per cent in 2012 and 65 per cent last year, with the report revealing the target was only met at Calvary public last year.

Chief Minister Katy Gallagher said the report was an important snapshot into how the ACT's public hospital emergency departments performed in comparison with similar-sized metropolitan hospitals such as Westmead, Gosford, Wollongong and John Hunter.

About 63 per cent of patients have been seen within benchmarked times so far this year.

''While this report shows similar results to other reports – that the ACT is continuing to show gradual improvements in the reduction of waiting times in ED – it also gives us an important marker in how long patients are waiting in the ACT when lined up against sister hospitals in other states," Ms Gallagher said.

New federal Australian Medical Association president Brian Owler said the report shows some jurisdictions were doing relatively well in terms of the National Emergency Access Target, but there were some that were not doing as well and "ACT is probably one of those that hasn't reached their targets".

"The target time is important because what it's designed to do is reduce overcrowding in emergency departments," he said.

"Overcrowding is associated with adverse health outcomes so getting people into an appropriate bed to get appropriate treatment in the appropriate part of the hospital is what the NEAT target is actually all about, so we don't have people clogged up in our emergency departments.

"The real issue now is that while there has been a lot of investment in terms of facilitation, primary and capital works, the reward funding under the National Partnership Agreement is going to cease – I understand there was $100 million in total in reward funding that was available but under the budget, that has now been cut. That means the incentives that have been there for various jurisdictions to try and drive the NEAT target performance will disappear."

report shows more than 120,000 patients passed through the emergency departments at Calvary and the Canberra Hospitals last year.

Ms Gallagher said: ''I am pleased to see that the government’s investment in new beds, medical professionals and strategies that are being rolled out across the hospital network are achieving results.

''The ACT government is committed to building on these results and continuing to strive towards meeting national benchmarks under the National Health Reform Agreement.”

Performance Authority chief executive Diane Watson said that while there had been considerable improvement for some peer groups and hospitals, the report was an opportunity for hospitals to learn from their peers.

Associate Professor Owler said changes announced in the budget would also mean less funding for public hospitals, compared with what was previously promised.

"I understand the government is only going to fund CPI (consumer price index) plus population growth, which is going to be a long way short of most states' budgets," he said.

"States are not going to be able to afford to fund services like emergency departments, and I think it's going to put a lot of pressure on emergency department performance, which actually does make a difference to patient outcomes."