The report, released by the Australian Medical Association on Thursday, contained little good news for the government, with 48 per cent of emergency department patients seen within recommended time.

Despite acknowledging significant improvements in the waiting times for elective surgery, the association described the performance of ACT emergency departments as "disappointing".

The government's latest annual report found 40 per cent of patients needing urgent care were seen within targeted times, with 69 per cent of semi-urgent patients waiting longer than hospital guidelines.

ACT AMA president Dr Liz Gallagher said hospital funding would be a key issue for both sides of politics, with a territory election scheduled for October 15.

"Health is always one of the hot topics in an election and both sides of politics know this is going to be a political issue," she said.

Canberra's troubled emergency departments have struggled to cope with a dramatic increase in demand. The number of people visiting the departments has increased by 22 per cent since 2009-10, despite the territory's population growing by 9 per cent.

The departments recorded their busiest year on record in 2014/15, with staff treating nearly 130,000 patients, or an average of 357 presentations a day.

The government has allocated $23 million to an expansion of the Canberra Hospital emergency department, with the $10 million first stage set to open on February 3 with an additional five beds.

According to Health Minister Simon Corbell, the expansion will increase the capacity of the southside department by 30 per cent when it is completed later this year.

In February, construction will begin on a $5 million paediatric streaming function with a separate waiting area and two consultation rooms for children and adolescents.

The median waiting time for elective surgery in the ACT is now 45 days compared to 35 days nationally, despite recent improvements.

Currently, 69 per cent of category two elective surgery patients were admitted within the recommended time, compared with 73 per cent nationally.

"While the improvements in elective surgery are welcome, along with the recently announced new beds in the emergency department at Canberra Hospital, the fact is ACT public hospitals continue to struggle to keep up," Dr Gallagher said.

In response to the report, ACT Health Minister Simon Corbell said there was a crisis of funding for the states and territories because of the federal government cuts to national partnership agreements.

"It is $600 million less for our public hospitals over the next 10 years, and that can only have a detrimental impact on public service delivery," he said.

Despite describing the ACT results as disappointing, Dr Gallagher also criticised the federal government and said the challenges facing the ACT could become worse.

"The Australian government must to play its part in fixing the problem, considering that federal funding to the ACT is projected to fall from $316 million in 2015/16 to $308 million in 2018/19," she said.

"If not corrected, an inflation-adjusted cut of some 8.8 per cent to ACT health funding demonstrates that the problem is likely to get worse before it gets better."

Mr Corbell said the territory government had increased funding year-on-year and would release a new project to "significantly reduce, if not eliminate, the long wait list for people needing elective surgery".

He also said the ACT had seen improvements in category one and category three patients for elective surgery, while category two had gone backwards.

A report presented to the ACT Legislative Assembly last year found the number of people waiting longer than recommended for elective surgery had increased to 1355 in 2014-15 from 726 a year earlier.

This is despite ACT public hospitals performing 11,875 elective surgeries in 12 months, the highest figure recorded and a 1 percent increase on 2013-14 records.

Opposition Leader Jeremy Hanson said Canberra's health system was in desperate need of more support. He accused the government of blaming everyone but themselves for the latest report.

"This situation has been going on for some time and is simply unacceptable," he said.

"What this shows, without doubt, is that Andrew Barr is not making health a priority, and he is not providing enough resources to the health system."

- with Katie Burgess