Figures in the 2017-18 ACT Health annual report show a sharp drop in key emergency department  and elective surgery wait times.

The annual report puts the blame on the blow out on a bad flu season and an increase in demand for surgery.

The government said there were "challenges" in managing demand for elective surgery in the ACT last financial year, with more people added to the waiting list than removed.

It said there was increased demand in emergency and elective surgery which hampered its attempts to reduce the number of patients waiting longer than clinically recommended for surgery.

"Workforce issues in the attraction and retention of surgeons and anaesthetists in the public sector are a key challenge, most notably in the specialties where waiting times are longer," the report read.

Other areas with staff shortages included ear nose and throat specialists, vascular and plastic surgery as well as surgical trained nurses.

The report pointed to additional funding announced last year for elective and emergency surgery as was the wait times were being addressed.

The number of publicly funded surgeries completed in Canberra grew about four per cent to 18,500 last financial year.

In the last financial year 91 per cent of urgent elective surgery cases were admitted on time.

In the same period only 70 per cent of semi urgent elective surgery patients were admitted on time and 77 per cent of non urgent patients.

That was a significant reduction from 2016-17 when 81 per cent of semi urgent elective surgery cases were seen on time and 88 per cent of non urgent patients were seen on time.

Canberrans are also waiting longer to be seen in the emergency department, with the percentage of patients being seen on time dropping significantly in a number of key triage categories.

Only 37 per cent of category three patients - who are considered to be in potentially life-threatening conditions - were seen within the recommended 30 minutes of arrival.

In 2016-17, 50 per cent of patients in that same category were seen on time.

At Canberra Hospital, just 28 per cent of category three patients were seen on time while at Calvary Public Hospital that figure was 48 per cent.

The report put the blame on the wait times blow out on a severe flu season.

"ACT [emergency departments] did not meet the target for categories two, three and four, due to growth in the number of hospital admissions and unprecedented seasonal demand with the severe influenza incidence in winter 2017," the report read.

"These impacts were compounded by an increase in the complexity of patient presentations, as demonstrated by higher numbers of categories one, two and three presentations and lower numbers of category four and five presentations."

Both Canberra and Calvary Hospitals also missed the targets for the optimal length of stay int he emergency department.

The hospitals aim for 90 per cent of admitted patients to be in emergency for four hours or less.

But at Canberra Hospital just 59 per cent of patients met that time period while at Calvary it was 72 per cent.