But a new report shows that Canberra's often-maligned emergency departments treat and discharge patients more quickly than many similar metropolitan casualty units in Australia.

Chief Minister and Health Minister Katy Gallagher said she did not expect the ACT to meet a target of having 64 per cent of emergency department patients treated and sent home, or admitted to hospital, within four hours of arrival.

Ms Gallagher said she was continuing to have discussions with the federal government about whether the ACT could still access $800,000 in reward funding linked to the target.

It would be unfair for emergency department staff and patients to be punished for problems related to the data doctoring affair. ''I've been trying to make sure that we support them and that's been the basis of my conversations with the Commonwealth,'' Ms Gallagher said. ''They've been very understanding, given the issues at Canberra Hospital.''

Ms Gallagher said health administrators had believed the hospitals had been on track to meet the target until emergency department data tampering by hospital staffer Kate Jackson had been discovered in April.

A report released on Friday compares the performance of the Canberra Hospital and Calvary Public Hospital emergency departments' interstate counterparts.

The ACT usually receives poor emergency department waiting time results when compared with other states and territories.

But the results appeared better when the ACT hospitals were compared against other institutions deemed ''major metropolitan'' by the National Health Performance Authority.

The report found that in 2010-11, 54 per cent of Australian major metropolitan hospital emergency department patients were dealt with within four hours.

The Canberra Hospital dealt with 54 per cent of ED patients within the four-hour target and Calvary Hospital had a 63 per cent success rate.

Best performer Royal Perth Hospital discharged or admitted 91 per cent of patients within four hours, while last-ranked Princess Alexandra Hospital in Brisbane only dealt with 45 per cent of patients within the target time.

The Canberra Hospital's result was better than that of the John Hunter Hospital in Newcastle (46 per cent)but not as good as Geelong Hospital (56 per cent).

The time it took for 90 per cent of admitted patients to depart the ED for a ward was 14 hours and 17 minutes at The Canberra Hospital and 13 hours and 49 minutes at Calvary Hospital.

The national result for all major metropolitans was 14 hours and 59 minutes.

Ms Gallagher said major metropolitan hospitals had longer ED waiting times because of the number and complexity of cases they saw.

She said the fact that the ACT had no smaller public hospital emergency departments sometimes led to unfair interpretations of performance results.

''It always hard when you measure it on jurisdiction. We're always going to struggle because we don't have small country hospitals that see three patients a day and they see them all on time,'' Ms Gallagher said.

''I will never stop arguing for respect for our public health system because it is so good, even if against certain measures there is room for improvement.''

National Health Performance Authority chief executive Diane Watson said fair comparisons gave similar hospitals the opportunity to learn from each other and improve their performances.

''When faced with information fairly comparisoned and they see in practice variations in the percentage of patients leaving at four hours, that's when they'll identify opportunities for learning,'' Dr Watson said.

The report grouped 134 public hospitals with emergency departments into the groupings major metropolitan, major regional, large metropolitan, large regional and medium. Large regional departments were most likely, and major metropolitan least likely, to discharge or admit patients within four hours.