It comes after a report by the Australian Council on Healthcare Standards found Canberra Hospital failed to meet standards in 33 of 209 core criteria, with some failures putting patients at "extreme risk".

The hospital must fix the long list of issues by July in order to keep its national accreditation.

Minister for Health Meegan Fitzharris said not being accredited was "not an option", but did not identify what would happen in the case it could not rectify the issues.

"Those are options we would discuss with the healthcare standards authority," she said.

"We are focussed on [accreditation] taking place and we will do everything we can to make sure we meet that in July."

ACT AMA president Professor Stephen Robson said hospital staff were frustrated that good clinical care was hampered by poor governance and management issues.

Dr Robson, who is also a visiting surgeon at the hospital, said junior staff had been preparing meticulously for the accreditation and were disheartened by the report.

He said there was a sense that with good patient care but bad systems in place, the good work of clinicians would be overshadowed.

"When the governance is wonky it sends ripples through the entire organisation," Dr Robson said.

"There's been huge upheaval at ACT Health recently and a lot of balls in the air.

"Their accreditation runs out in July, unless they meet that it would be a bit of a disaster."

Despite the alarming results, Dr Robson said Canberra residents should be confident in the level of care they receive at Canberra Hospital.

"If you go in and you are cared for by a nurse, doctor, physio or anyone else, they are skilled people doing their best to do a good job," he said.

"The real issue is the tools they have at their disposal and the rules and processes they have to follow."

He said the AMA was blindsided by the government's recent decision to split ACT Health in two and part ways with director general Nicole Feely.

"My concern at the moment is it's not well understood," Dr Robson said.

"The nurses, doctors, everyone needs to understand who they are working for.

"Certainly with director general leaving suddenly and unexpectedly it engenders concern with everyone.

"We put a lot of effort into spending time with the minister, and executives and I have to admit it has been a bit perplexing to for us to see there seems to be a lot of projects started and not finished."

Opposition leader Alistair Coe put the blame for the concerning results squarely on Ms Fitzharris.

But he said he was confident the hospital would meet all the requirements to be accredited by July.

“There are clearly governance issues right across the organisation and simply doubling the costs by having two directorates is not going to be the solution," he said.

“The solution needs to be the minister making it very clear who is responsible for what so we can ensure that clinical decisions are made properly.

"However at present I've got no confidence that the minister is actually taking responsibility for the governance and integrity issues that exist within ACT Health."

Ms Fitzharris said it was clear there were governance issues within ACT Health that needed to be addressed.

She said the delineation of ACT Health would bring it into line with other jurisdictions across the country.

"We're obviously concerned and disappointed there have been 33 items not met," she said.

"We will take this as a significant opportunity to learn and improve."