Fewer than half of people going through the doors of Canberra's emergency departments were seen within the required time in 2018-19.

The latest Australian Institute of Health and Welfare statistics show the ACT's overall performance against key national indicators is in stark contrast to other jurisdictions.

The figures, which included Canberra Hospital and Calvary Public Hospital, showed ACT's median emergency department wait time was 50 minutes.

The next worst jurisdiction was Western Australia at 28 minutes.

Only 46 per cent of ACT's emergency patients were seen on time - again the lowest rate in the country.

Health Minister Rachel Stephen-Smith conceded waiting times were a challenge for the territory's hospitals, citing increased demand.

"We know there is more work to be done to ensure Canberrans have access to timely healthcare," she said.

Canberra Hospital's inability to treat urgent category patients on time appeared to be a major reason for the poor results.

Urgent - or category three - patients should be treated within 30 minutes of presenting. These patients make up a large chunk of all people attending emergency departments.

But at Canberra Hospital, only 25 per cent of urgent patients were treated on time.

The national average for major hospitals like Canberra Hospital was 57 per cent.

When compared to its peers, only Perth's Fiona Stanley Hospital was worse, where just 24 per cent of urgent patients were seen on time.

The only category Canberra Hospital was able to meet the peer average was in the emergency category.

ACT had the third highest median wait time for elective surgery at 48 days and the second highest rate of patients waiting more than a year for surgery (7.2 per cent).

Victoria was the best performing state for elective surgery with a median wait of 28 days.

ACT's emergency department performance showed a sharp drop off after the 2016/17 financial year.

In that year, it was still the worst performing jurisdiction but was within touching distance of others, with the median wait sitting at 30 minutes.

Ms Stephen-Smith said Canberra Hospital had "robust" strategies in place to create capacity and manage demand.

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"I can assure Canberrans that if they present to an Emergency Department needing urgent care, they will be given the care they need," she said.

"I have full confidence in the experienced and professional medical staff and clinicians who work to ensure all patients are cared for in the most clinically appropriate place and time. Feedback from consumers confirms that our hospitals provide high quality care to the vast majority of patients."

She said Canberra's hospitals had seen not only increased presentations, but more complex patients.

"To help address this, the government has put on more doctors in Canberra Hospital's ED and is investing in a significant expansion of Calvary's ED," Ms Stephen-Smith said.

Asked whether the hospitals were adequately funded, she pointed to almost $1 billion in health infrastructure investment slated for the next five years.